My understanding is that afl-cmin should retain every file that takes a different path.

that understanding is wrong :-)
afl-cmin retains the smallest file for each reachable edge value (e.g. edge 3 with 2 visits is a unique,edge 3 with 1 visit is also unique).
there is no MCDC measurement whatsoever.
This is still the minimization from the original vanilla afl from ~2016 or so.

If you want that, then you have to implement that yourself (IMHO it would be a good thing to have, so it is something I would happily merge from a PR).