Yes, I think the distance to wall with the stands on the ledge would be about the same as with FMBs -- far enough away from the wall that the rear port will be able to breathe OK, just not necessarily the optimal distance in all respects.
Given the size and shape of your room, I don't *think* you're going to have a problem anyways... and you're definitely better off with stands since you will have the ability to experiment with placement.
I think that's going to be a pretty good setup. I'm guessing the couch or chairs directly in front of the speakers will be pulled a few feet from the back wall so you can walk into the DR. If so, the M3s should be "big enough". I would be willing to bet money that you will end up with the stands on the floor, not the ledge, though... you just have to do something nice to make up for the lower WAF
