hello99,
I haven’t re-answered point #1.
1)”The only reason they would become assur is because of “ha’yotzei min ha’tamei”, and the Chavos Daas 82:2 says this does not apply to separate bria.”
Incorrect -the reason is because it has the status of its host. The reason worms become ossur in animals, Rashi says, is because of Ever Min Hachai. Worms from cheese are milchig. By the way, the Chavos daas is not matir, he makes it an issur d’rabonon.