I've been doing a lot of hunting and reading, trying to figure out if this can be done from the user's end of things, without having to have new plugins created, and have made a couple of interesting discoveries.
First, you were absolutely correct regarding the ability to add cover shots to the ID3v2 tag, and I've since located multiple programs that plug-in to various players and allow you to see them while the album plays (my favorite is CD Art Display: http://closetosoftware.com/forum --works with several leading players, and even the dreaded i-Tunes). MP3Tag worked great, and I was able to add the covers exactly as you said, and a quick test proved that the archives remained stable and the tracks could still be extracted. Brilliant.
Ah, but then I found something very interesting! There's a program called MP3cue that allows users to play tracks from bundled MP3 albums. It's not perfect at this point, because it was created with lumped, single albums in mind, not actual archives with stored tracks. As it stands right now, for people using Make it One, we'd have to load the unpacked tracks into Winamp (I think it's been ported to some other programs and platforms, too), then manually add each track into MP3cue. The finished sheet can be saved, and once you've got it, you can add it to the ID3v2 tag so that you don't have to keep the extra file around (although that works, too).
Clearly this is beyond tedious for anyone that's already got a lot of MiO albums. However, since we now know that the function exists and works, all that really leaves is the need to be able to create the cue sheets from the albums. So, what I'd like to suggest would be the inclusion of an optional checkbox in Make it One that, if enabled, would also produce a standard cue sheet along with the album being created at the time. Users could then quickly add any cover shots and cue sheets to the MiO archive's ID3v2 tag using MP3Tag, and bingo, it's all done.
The other cool thing about this is the fact we're dealing with standard, universal cue sheets, which means any other media players out there that chose to enable the function (reading the data from the tag) could do so easily.
Here's the link to MP3cue, if you'd like to look at it: http://www.guerillasoft.co.uk/mp3cue/index.html