Well, turns out that md5 alone isn't enough either.
Something strange did happen though. At first I thought it was a fluke. Then it happened a second, and finally third time, and I'm thinking it's a piece of the puzzle.
I was in at the main menu, windowed mode, having just left a game testing a mod. I rebuilt my mod, and gave it a new md5 while I was at it. I went back to the mod screen, and it wasn't in the list. I figured damn... guess it didn't work. I decided I would give it a minute or two to refresh, assuming it's doing some sort of polling of the file system. Came back, still not there. Oh well. So I go to delete the folder in the neighboring window. The moment I clicked on the mod folder, the still visible civ window immediately refreshed showing the rebuilt mod. I didn't delete, rename, or anything else the folder, I simply clicked on it.
EDIT: I've now rebuilt my mod at least a dozen times testing a variety of things, and just by leaving the folder highlighted in windows explorer, I haven't needed to quit civ 5 since trying this out.