I guess just collapse the Lemmy.world heading? (or filter that server out.) Not sure if it's implemented yet but seems trivial enough to implement if not already there. The comments are listed in a batch under the server heading, not intermingled.
I just joined piefed since it looks like it merges multi-instance posts with the same article URL. Not quite the same thing as consolidating communities, but great for bringing conversations from multiple communities into one place.
Sounds like you need a virtual machine for each Teams account!