Minecraft Version: 1.21.1
Mod Version 2.5 (refabricated)
Mod Loader: Fabric

The mod seems to be affecting biome tags that are not vanilla. I tested with Cobblemon 1.6 and noticed the End Island has the #Cobblemon:id_overworld tag. Removing End's Delight fixes this.
Could you take a look?

Do you mean #cobblemon:is_overworld tag? End's Delight shouldn't have modified any biome tags. I used /locate to test biome tags only with Farmer's Delight Refabricated and Cobblemon, and it showed that the End biomes have the #cobblemon:is_overworld tag. I'm not sure, but perhaps it was Farmer's Delight Refabricated that modified it.