I've found it's actually not awkward to use this way, but your personal preference may be different. It's fairly comfortable to hold with my right hand, get a good grip on the motor with thumb and 3 fingers, and use my pinky finger to trigger the shutter. Plus I don't have to hold my right hand up any higher above my face than if shooting landscape.
I've used the same MR-3 on my FM2/MD-12 combo, where it attaches in the more "traditional" position. Doesn't feel nearly as good to use as with the F3/MD4.