I'm playing ATM7 1.18.1 v0.2.36 which uses Apotheosis-1.18.1-5.2.2. I silk-touched a skeleton spawner from a DungeonsArise dungeon. I created a Mob Grinding Utils villager egg using a swab. I right-clicked the spawner with the villager egg. I also right-clicked the spawner with a comparator so that I could have redstone control over the spawner. I placed the spawner on the ground with a lever beside it. I could see the villager in the center of the spawner. I activated the lever. Sure enough, several villagers were spawned. However, the spawner reverted back to skeletons and suddenly skeletons were spawning. I repeated the entire process. Villagers spawned in the first spawning cycle but then skeletons spawned after that.

The actual issue for this is that the vanilla code for changing an entity only changes the entity of the current spawn potential - if you find a spawner with multiple potentials, it will only change one of them.

5.3.0 and onward will re-implement a fix to this by clearing all spawn potentials when a spawn egg is applied.