Yes the servers can determine each species (including whether humans) that players are allowed to play as.
The Primal Survival Total Conversion is being developed by Instinct Games, who also work with Wildcard on ARK: Survival Evolved itself. It will add a lot of new features for Mod creators too, giving them much more control over how players can interact with the game world (looking forward to Uber-TRex vs humans competitive game mod... if someone doesn't create it, I'll try to get around to it myself )
Cheers,
Jeremy