iTunes Match + manually managed music?

Solution 1:

Note that iTunes Match is fairly precise in how it matches songs. A unique recording will probably be uploaded, not matched -- certainly, if the unique recording has a different length than the standard ones, it won't be matched. If you are willing to potentially lose $25, get iTunes Match and see what is matched. If stuff that you want to be uploaded is matched instead, don't use iTunes Match.

Solution 2:

You could turn Match on on your computer and not on the iPhone. That would allow you to keep manually managing your music on the phone.

Ultimately, though, it seems like iTunes Match is not a good match for the way you use music, particularly the "unique masterings and recordings". If you've got $25 to burn and you're willing to experiment, back up your library (and iTunes preferences) and turn it on. If your music disappears or comes back in a way you don't want it, turn Match off and restore your library and preferences.