Now that I've actually gotten around to chopping this up for the omnibus...
Due to the framing device showing Bel in the Empress Mia timeline instead of the Empress Prelate timeline, I think it should go after the end of Volume 11 (where Bel 1 is shot and Bel 2 replaces her), at the end of To The Moon-Led Morrow.
It looks like stripping the duplicates out still leaves enough chapters left that we won't have two intermissions next to each other or anything, so I think the collection's still readable without them.
On a related note, I spotted at least one pre-pub bug report that doesn't seem to have been addressed before the ebook was published. I wasn't even looking for that, but when you have both copies of The Mystery of the Island and the Sage of the Moon on screen at the same time, it really jumps out at you.