A lot of the pokemon that spawn using evolution stones spawn however some do not even though they use the same stone, lacking consistency.
For example Clefable and Delcatty both use moon stones to evolve however, why would a Clefable spawn but a Delcatty not?
I have always thought the mod was loosely based on the game, with some allowances for the quirks and gameplay elements of minecraft.
Like being able to catch other starters. Where their would be no way for players playing on singleplayer to catch other starters and it would make for poor gameplay aswell.

The evolution stones don't follow this rule however.
For one, they are already a gameplay element requiring you to take time and a little bit of knowledge to hunt down some of the stones making them a semi rare commodity.
Being already established as a ingame gameplay element to let people get these rare pokemon adds gameplay value and is in no need to be supplemented by random spawning.
And two, Even in the game they were pretty rare, and never spawned naturally. Think about It, out of the like 800 pokemon only like 4 even use a firestone. But in pixelmon they just spawn randomly so you don't even need one. To catch one of these rare pokemon significantly diminishing their intrinsic value.

This is also tied together with the trade evolution pokemon which also like the evostone pokemon never spawned naturally in the games.
However unlike evo stones in singleplayer their would be almost no way to get some of these trade pokemon.
Their is also some inconsistency's with the trade pokemon spawning aswell, for example why does Gengar spawn but Golem does not?
If Gengar was added to let people in singleplayer catch one without trading then what about the pokemon that require items, like Porygon-Z or Milotic.

A lot of these spawns seem pretty half thought though like accidentally adding in half of the eveelutions, and the inconsistency would lead me to think its a bug. So a solution would be to have a separate spawner json for the server.jar that disables tradeevo pokemon spawning and to not allow evostone pokemon to spawn ingame.

This should be getting reworked soon. There's been a lot of discussion on this internally as of late, thiiiink we've got a system for this now. Check back when the new update hits, things should be better then!