Forge 1.12.2-14.23.5.2838
Apotheosis-1.12.2-1.10.5
i'm on a custom modpack, but i don't know if it changes anything, i'll test with only apotheosis later and edit.

When i use a nether star on a spawner, if i update the spawner (restart server, break it etc..), it also apply the "ignore spawn cap" in addition to the "ignore player", if i remove it with chorus fruit, it removes it until next update of the block, only way to remove it completely is with the nether star....

I'm getting this same issue with a spawner in version 1.10.5. We're on a dedicated server and the spawner is spawning infinite villagers unless we remove the nether star upgrade, we can temporary disable it by inverting a chorus fruit but as OP said reloading chunks/server causes it to regain the spawn camp. A great way to test this is silk touching the spawner as even breaking the spawner casuses it to reappear.