I fixed this on a branch I'm working on, will share it tomorrow. I just ensured that the dir exists whenever a Mutagen command is called (and memoized the function that creates it to ensure it's only called once during execution). But maybe we want to do this up front.
Note: The new Mutagen sync monitor does ensure that the dir exists when it starts, but I noticed a couple of edge cases where errors would occur when e.g. listing syncs without the monitor having been started first.