I think we should stick to the dex number and name because in essence, they're all the same Pokemon. And I guess the answer to this question is just an opinion to everyone on whatever they wish the species clause should be.
If you have to treat for different versions of the same mons differently, then they're not the same pokemon.
Just look at Deoxys, Shaymin, and Giratina. Deoxys-A dishes out power from it's 180/180/150 offensive stats while deo-D takes hits with its 50/160/160 defs. When building a team or facing a Deoxys-D, nobody would be taking LO Psyshock's and Superpowers from 180/180 Special Attack and Attack. You'd instead expect to take Toxics and Seismic Tosses, and for preparing a team with Deo-A, you should never aim to 2hko/3hko a Deo-A with anything. Giratina is in a similar boat with its regular form designed to take hits and its origin forme expected to deal hits. Also, I doubt you would see very many people on ladder spamming air slashes and Seed Flares for drops and flinches with Shaymin-L as you would see people spamming those moves with Skymin and Serene Grace.
Personally, I see no issue to revising the species clause to "A player cannot have two or more pokemon with the same national dex # and the same forme allowed on the same team." It allows more choices of teams and might lead to some interesting metas and games.
Edit: It did not come to my mind while I was originally posting the proposal, but my intent in proposing the revision was not to include Gastrodon since the difference between the two formes is aesthetic. There is no difference in base stats, movepool, ability choice, or typing (qualities that influence a competitive battle). Another possibilty that was not intended is having two Basculin. Since Basculin's forme changes on ability/version, it also shouldn't matter. That's like looking at a Venusaur or Alakazam and figuring out what gender it is by looking at its sprite.
If the only difference between two formes of two pokemon that share the same Nat. Dex # is the appearance, then they aren't considered two different formes.