So I just saw the backrooms move and I have a theory. And warning, spoilers ahead
The bacteria and captain clark not only aren't the same entity, but were both competing for status in the backrooms with captain clark being the more dominant entity, well was now that it is dead. My guess is that the bacteria was a competitor for territory and power within the backrooms with captain clark being the dominant and apex entity that had no equal despite the bacteria existing.
My reason is that the other entities seem to fear captain clark, and the fact that clark (regular clark) drew it on a golden throne, as if it was the leader and ruler. The bacteria and captain clark not being the same would give way to why the bacteria wasn't in the movie, because they weren't in its territory, they are in captain Clark's.
As for why captain clark attacks clark even though it didn't before I don't have an answer for, best guess is that captain clark might take on suppressed characteristics that regular clark had and that the sudden attack was one of them












