Permit me to reply to your question as if I were an FM3A user, since I am an FM2n user, and have used an FE and FE2 in the past, and all these cameras are part of the same family:
The DK-3 eyecup, because I wear spectacles much of the time (the diopter correction eyepieces meant having to hang my spectacles around my neck with a neck strap, which I dislike, and which meant that the spectacles could always be damaged by the two dangling cameras). What really freed me in this respect, however, was the HP finder of my F3/T (but that's a different story). Failing that, though, the DK-3 was always my best bet for making the most of the FM2n's (and by analogy FM3A's) focusing screen.
The MD-12 I do not dislike, but for sheer ergonomic success I find it inferior to the MD-4 for the F3, and even (hear, hear, since we're talking heavy! the MD-3/MB-1 combo for the F2.
I had the MD-3, John... Not the MD-2, alas! Anyway, don't make much difference now; my F2A is in other hands! And I am a richer 'Nikonian' for having tried and tested it for a few months. A great, great camera, pity we didn't hit it off, the "two of us". Instead, the F3(/T) stole my heart. Who would have thought of it? Funny thing is, you are to "blame", in substantial measure!
I would certainly add the MD-12 for completeness but if I have one I doubt that I would use it much. The FM3a+MD-12 combo isn't as great as the F3+MD-4 combo. The strength of the FM3a are its cuteness, compactness and operation without battery.
The MD-12 is worth the weight just to keep the advance lever from sticking out. When I want to meter it is usually pushed in. When I want to shoot it's brushing my cheek. The camera is always ready with the MD-12. Please don't blast me for having an F100 in my signature.
A question rather than an answer: is the eye relief on the FM3 any better than the FM2? I had an FM2 many years ago and got rid of it when I had trouble seeing the total finder with glasses. Switched to F3HP.
Alas, there's no difference. I've about given up shooting with glasses and just use diopters instead. It's more comfortable for me, since even the Lenscrafters featherweight frames seem to weigh down the bridge of my nose too much. Next time, I'll try the frameless glasses. Friend of mine has a pair. Probably 1/4 the weight of mine, even though mine are very light. -J