I don't see why it would be incompatible with anything else you've got - essentially the MFM is just adding (a lot of) additional ships to your game, not altering stuff that's already there or that has been added in by other mods.
However because of the large number of ships being added (and therefore loaded by the game every time you run it), it does put quite a strain on your system resources. The #1 obstacle to running this mod from what I've seen here is not conflicts with other mods, but lack of RAM. If that's a problem after enabling the MFM, it will most likely manifest in a CTD when you are trying to load a patrol. If that occurs my first suggestion would be to disable it and try the Lite version instead.
Also look into the 4GB patch for the game .exe file if you have not done so already. Many people find that they cannot run the MFM at all without the patch.
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