Why does species clause still apply to regional forms?
I think it's rather clear that regional forms of mons are different enough from each other to be considered different mons.
To me it seems like this is an oversight that's not been addressed due to a lack of interest from players, or perhaps so as to not shake up what is a fairly stable metagame.
But if there is some other logic behind this application of species clause I'd be interested to find out what that is.
This is just how it works on cartridge and since Pokemon Showdown is a similator it takes most elements implemented on cartridge. Now, you could do some sort of species clause that counts regional forms as different Pokemon, but this seems very specific (and a general rules counting all forms of a Pokemon as different Pokemon won't make much sense because you would be able to play several Silvally/Arceus for instance) and most of the time Regional forms are still very close to the other form with just a different typing and some new Moves.