RG4N says "Yes." This is the most important claim in its court petition. RG4N makes other claims, of course, but this is the only claim that would (a) entitle it to a hearing before City Council; and (b) make approval of the site plan discretionary rather than a matter of legal right.
I think the answer is "No," but I will set out the relevant ordinances and let you make up your own mind.
RG4N is correct that the Northcross site is zoned GR (General Retail), correct that a garden center is a "plant nursery" for zoning purposes, and correct that a plant nursery is a conditional use in GR districts.
But it has ignored the main issue. The City says the proposed garden center is permitted as an "accessory use." If the City is right, then the garden center did not require a conditional use permit, and RG4N was not entitled to a hearing before City Council after all.
Is the Wal-Mart garden center an accessory use?
Let's look at the two relevant ordinances:
An accessory use is a use that:
(1) is incidental to and customarily associated with a principal use; [and]
(2) unless otherwise provided, is located on the same site as the principal use[.]
A commercial use such as a plant nursery must satisfy extra requirements. Specifically:
A commercial . . . use that is otherwise prohibited in the zoning district is permitted as an accessory use if the use:
(1) is operated primarily for the convenience of employees, clients, or customers of the principal use;
(2) occupies less than 10 percent of the total floor area of the use; [and]
(3) is an integral part of the principal use[.]
There are six criteria between the two ordinances: (1) an accessory use must be incidental to the primary use; (2) it must be customarily associated with the primary use; (3) it must be located on the same site; (4) it must be operated primarily for the convenience of the employees, clients, or customers of the business; (5) it must occupy less than 10% of the total floor area of the use; and (6) it must be an integral part of the principal use.
Most of these are beyond dispute. Garden centers are commonly (i.e., "customarily") included in big-box retail (#2). The proposed garden center would be located on the same site as the Supercenter (#3). It would be operated primarily for the convenience of Wal-Mart customers (#4). It would take up less than 10% of the Supercenter's floor space (#5). (I'm crediting City staff with the ability to correctly calculate the relevant floor areas.)
Perhaps RG4N disputes that the garden center is "incidental" (#1). A tertiary meaning of "incidental" is "inessential," and RG4N does allege that garden centers are "essential" to Wal-Mart Supercenters. But it makes no sense to permit a principal use and then exclude essential collateral uses. No, in the context of accessory uses, "incidental" means "minor" or "subordinate to," either of which is a fair description of garden centers in Wal-Mart Supercenters.
This leaves "integral" (#6), which is what I initially assumed RG4N would dispute. One meaning of "integral" is "essential," and I doubt that a garden center is really essential to a Wal-Mart Supercenter. I think "integral" here probably means "constituent" rather than "essential," but still I figured RG4N would make the argument. But RG4N evidently decided to go another way since it admits that "[g]arden centers are integral components of big box Wal-Marts . . ."
It does not appear that RG4N will seriously dispute that the garden center satisfies the criteria for an accessory use. So what will it argue?
RG4N's petition does not say so we have to guess. But I think this sentence in the petition is a clue: "A plant nursery is a use that is not prohibited under GR zoning, but instead one that requires a conditional use permit from the Zoning and Platting Commission." That's a strange statement. Why go out of your way to say that the use you are objecting to is "not prohibited" on the site?
Here's my guess. The ordinance defining commercial accessory uses states that "a commercial use . . . that is otherwise prohibited" is an accessory use if the various conditions are satisfied. I think RG4N will argue that a conditional use is not "prohibited" -- after all, it could be authorized -- and therefore cannot be an accessory use.
The problem with this is that all conditional uses are "otherwise prohibited" unless approved by the Land Commission or City Council. A conditional use will either be approved -- in which case it does not need to satisfy the accessory-use criteria -- or it will be denied, in which case it is "otherwise prohibited" and qualifies as an accessory use. A hearing would be an empty formality. Why read the ordinance to waste Council's time? The more natural reading of the ordinance is instead, "Even if a commercial use is not permitted under other provisions, it will be permitted as an accessory use if . . . "
By definition, an accessory use is a relatively minor, typical component of an acceptable primary use. If the primary use is acceptable, the collateral use will likely be acceptable too, which is why the Code permits accessory uses as a matter of right without a hearing. But if you were worried that some accessory uses might be objectionable, you would not single out conditional uses. A use is classified as "conditional" only if it is potentially compatible with the other uses in the district; conditional uses are judged and approved under a relatively lenient, discretionary standard. Uses that are flat-out "prohibited" -- i.e., uses that are neither permitted nor conditional -- are presumed to be so incompatible with the other uses in the district that they require either a variance or an amendment to the zoning code. It makes no sense to insist that relatively benign conditional uses get special permission while giving a free pass to uses that are presumptively inappropriate for the zoning district.
I think it is pretty clear that "otherwise prohibited" refers to any use that is not a permitted use. But suppose RG4N convinces the court that its interpretation is reasonable too. Its very best case then will be that the ordinance is ambiguous. It will still have a big problem. When an ordinance is ambiguous, courts give serious consideration to the interpretation of the officials charged with enforcing it. In other words, the court will largely defer to the City's interpretation in deciding whether a conditional use can be an accessory use.
What this means is that if the City has treated conditional uses as accessory uses in the past, RG4N will almost certainly lose. Despite RG4N's insinuations that City staff is in cahoots with Wal-Mart, I don't think the City would change its interpretation of the ordinance mid-stream just to approve the Wal-Mart site plan. I also suspect that if the City had given the ordinance conflicting interpretations in the past, we'd have already heard about it in a press release.
Exhausting Administrative Remedies
RG4N also faces a procedural obstacle. The Land Development Code gives the Director of the Neighborhood Planning and Zoning Department the authority to determine the appropriate use classification for an existing or proposed use or activity. People who disagree with that determination may appeal the classification as "interested persons" to the Board of Adjustment. Decisions of the Board of Adjustment can then be reviewed by a district court.
The right to appeal Director classifications to the Board of Adjustment is what courts call an "administrative remedy." Courts take administrative remedies very seriously. So seriously, in fact, that they usually will refuse to hear a litigant's claims if he refuses to exhaust his administrative remedies.
The Director has classified the garden center as an accessory use. To my knowledge, no one has appealed that classification. The claim should be thrown out for failure to exhaust administrative remedies. Even if an appeal was filed, then the claim should still be thrown out (or at least abated) because it is not ripe until the Board of Adjustment has ruled on it. I don't see how a district court can consider the conditional use claim on this record. (If I'm missing something, I'm sure somebody will point it out.)
A final point
It's worth noting that this debate over the accessory use ordinance has nothing to do with the real objections to Wal-Mart. Who objects to the Wal-Mart just because it will have a garden center? I haven't seen any "No garden center at Northcross" T-shirts. The fact is that the garden center is the only hook RG4N can find for demanding a hearing before Council. It has identified a potential ambiguity in the Code that it thinks it may be able to exploit to get its way. In other words, it is relying on a technicality (erroneously, IMHO). Bear this in mind the next time RG4N accuses Lincoln of exploiting "loopholes" (such as ignoring ordinances that were enacted months after it filed its site plan).
Postscript. RG4N held a meeting a week or so ago to explain its claims. I didn't go. If you were there and heard any of these points addressed, I'd appreciate it if you'd comment.
 City of Austin Land Dev. Code s. 25-2-891.
 City of Austin Land Dev. Code s. 25-2-894.
 RG4N Petition par. 33.
 City of Austin v. Hyde Park Baptist Church, 152 S.W.3d 162, 166 (Tex. App. -- Austin 2004) ("If the meaning of an ordinance is doubtful or ambiguous, we will give serious consideration to the construction given it by the governmental body charged with its enforcement or administration."); Zamora v. City of Austin, 2002 WL 31769039, *3 (Tex. App. -- Austin 2002, pet. denied) (affirming Board of Adjustment ruling which chose between two competing interpretations of CS zoning requirements regarding the permitted use of the property).
 City of Austin Land Dev. Code s. 25-2-2(A).
 City of Austin Land Dev. Code s. 25-2-2(C).
 Currey v. Kimple, 577 S.W.2d 508, 513 (Tex. App. -- Texarkana 1978, writ ref'd n.r.e.) (holding claimants could not challenge issuance of building permit where they had not appealed permit to Board of Adjustment).