Regarding 1.00o vs. BC, I think what I might do is take advantage of some of the unused bytes in Data1 and just stick a flag in there somewhere to indicate what kind of file it is, probably for the BC levels. It wouldn't work for the original three (Binnen, Rain, Boss), but it'd work for anything made afterward.

An issue I see with only one copy of MLLE on a computer (as spread among multiple games) is that it wouldn't work very well for starting new levels, since where would you get the list of tilesets from?
ETA: Duh, each version profile .ini could just include the filepath. Hmm. I guess putting everything in one folder will work, and hopefully it won't slow down loading times overmuch. Problem solved?