I been having a bit of a perplexed trying to get anything tweaked for any animal that spawns with this mod.
Any attempts to change spawn weight doesn't seem to affect anything as I had tested this with Does with a spawn weight of 0
and Boars with a spawn weight of 100, with the result being seemingly normal generation despite the expectation being little piggies conquering the pitiful world we call minceraft after their carnage on the innocent Does.
The animals don't care if the biome blacklist is true/false as they will still spawn in the overworld like the sassy beings they are.
They exist just to spite everything even when their spawning is set to false.
I was going to write something silly for spawn count, but you get the gist of this point.

This has all been tested with verisons 1.16.4-1.2.5 and 1.16.5-1.3.0

I can confirm as of stone-age-1.16.5-1.3.2.jar this issue still persists.

For example:

#Remove spawning of vanilla animals like cows, pigs, sheeps
	removeVanillaGeneratedAnimals = false

Is completely ignored. Still none vanilla animals spawn.

And this:

["mob spawning".deer]
		#Enable spawning of mob
		spawnDeerEnable = false
		#Spawn weight of mob
		#Range: 0 ~ 100
		spawnDeerWeight = 20
		#Spawn min count of mob
		#Range: 1 ~ 100
		spawnDeerMinCount = 4
		#Spawn max count of mob
		#Range: 1 ~ 100
		spawnDeerMaxCount = 10
		#If spawnDeerAllowedBiomes is blacklist
		spawnDeerAllowedBiomesBlacklist = false
		#Spawn deer in allowed biomes
		spawnDeerAllowedBiomes = []

Is also completely ignored. I even tried with an empty allowed biome list and all your mobs are still spawning.

I have tested this on a server.

Request reopening this issue please