If 3.1 is your thing, most receivers will recognize the absence of the surround speakers and down-mix that information into the front right and left speakers.
Other posters are right - letting the dual M3s act as a phantom center would work quite well. It might help with your overall sound during dialogue scenes, in fact.
If you insist on the center channel (which I would endorse), don't worry too much about boundary effects, etc. Just put it in the cabinet and give it a whirl. If the coloration (which I predict will be minimal to non-existent except to the most well tuned ears) bothers you, then you can work on damping and other techniques to minimize the impact of the cabinet. Just plug it in and enjoy, mostly, though. Try to not focus on all the bad stuff - most of which isn't detectable by your average Joe.
I would also echo the advice to consider a set of QS4s or maybe a 5 piece matched set of M3s (two of which could be used as surrounds). WATCHING movies is probably less than half of the experience. While our eyes are more accute to subtle detail than our ears and while our eyes can detect imperfections easier than our ears typically can, it is the sound that really envelopes you in the movie/tv/music experience, making the illusion complete.
There are lots of attractive options offered by Axiom (including custom finishes) that make the surrounds less obtrusive in the decor. I got surrounds with a different finish (Light Maple) because they blend in better on the walls than would a Cherry Finish (which I have up front).
