Hey @iSivert , sorry for the delay! 
We have a new release for you, which should have the disappearing custom mesh issue addressed.
Please get it here and have a try.
About this one, sadly there is no quick fix from our side for the time being.
But we do have a workaround. What we need here is one extra Library Override, down to Armature data.
Please have a look at my video recording, note that I added one more override on the Human Armatrue for each rig, via menu Library Override > Make > Selected.
Hope this works for you. And thank you for your patience!
Oh, and. About that Human.001.rag, it was just copied from Human.rag so that it matches armature name (I believe this is also what you are already doing), a bit tedious. We should have this workflow smoother in the future.