I've been trying to figure it out for the past 20 minutes, and still can't get them to at least get into Advanced Hive. Can somebody help me with this?

If they don't want to get into the hive, they might be bugged. I'll look into that.
Can you try with a freshly spawned ender bee and see if it behaves differently?

I see what the error is now, they only feed on chorus flowers and probably wont get into the hive without filling their bellies.

Tried to: Breed an ender bee and just put tons upon tons of flowers (mainly poppies) around the Advanced Hive - Did not work
Spawn ender bee from spawn egg and do the same with flowers - did not work
Tried to spawn ender bee with commands and do the same with flowers - did not work
Tried everything above but on super flat world - did not work too
So yeah, definitely bugged. But thanks for responding! Hope working on the mod goes well!