Funny, I’ve been brainstorming ideas for almost the exact same scenario recently and also came up with the Aux project idea.
In our case, the user we’ll have isolated will only be doing drafting, which makes things a little easier. The team both wanted to keep a number of different drafters from knowing about each other (which may end up with a couple Aux project).
A supervisor will then need to copy his work out of the Aux project and into the main one, which will require either using the Compare Versions tool as you suggested or just knowing where the drafting is happening and cutting/pasting.
One extra detail is that they wanted the Aux project to have access to Biblical Term rendering choices. So the ProjectBiblicalTerms.xml file will periodically need to be copied from the main project folder into the auxiliary one.
Anyway, I don’t have any ideas that you haven’t explored, but I’m also quite interested in hearing if other people have best practice ideas for this sort of situation.