Incorrect. Refer to the Fair Use agreement to the Minecraft Eula - https://account.mojang.com/documents/minecraft_eula
Additionally, not that assets isn’t the issue - all Pixelmon code, models, resources, and everything else was done custom. The stuff that’s just “some internal code that references Pokémon names” is the same stuff that violates copyrights and led to the C&D in the first place.
Mojang was copied on the C&D and is well aware of Pixelmon’s status as being illegal. If they choose to act upon it, server can legally be closed or blacklisted.
However, I for one do not forsee that as a likely possibility. I know that while many servers have cloesed, many more have remain open. In some ways, this has actually brought together the community - what happens next is yet to be know.