I never really looked at the requirements, but I don't see why someone couldn't go for MMR as a 3 rail O person, the requirements don't preclude that. The only issue might be with the scratchbuilt motive power, that it would require building a scale model, and you might have a lot less detail parts available commercially than let's say HO, but the same would be true of O 2 rail. The scenery section applies to 3 rail as well as 2 rail scale, and the layout construction section doesn't seem to say everything has to be scale, the point seems to be about the craftsmanship of the stuff the person builds, not whether everything on the layout is scale perfect, etc.
About the only obstacle I could see would be if those evaluating the work of the person held it against them they worked in 3 rail (were modelling snobs in other words), but to be honest I have met more than my fair share of 'serious modellers', including ones well known in the NMRA and in magazines like Model Railroader, and found very few snobs who would turn their noses at anything three rail,no matter how well made, most of them would enjoy someone doing great work in no matter what scale/gauge/number of tracks they worked in *shrug*. I see a lot more friction around the issue of operations versus those who like to 'run trains' than with this particular issue.
For me if I were to go for the MMR it would be about meeting those challenges, having something laid out in front of myself can motivate me to try and achieve what they talk about, though I doubt I would ever go through a formal process to get the certificate, and honestly if going for the MMR it should be about the fun of doing it, not worrying if they will 'let you' achieve it
. The only negative thing I could think of being MMR certified would be if some people would be afraid to approach the person with their attempts at modelling, afraid that they would make fun of their attempts as being lesser (sadly this does go on with other things that offer certification paths,), which would be ironic because from what I can tell the MMR is in large part designed to create a group of modellers who are not only skilled, but also are there to share this with others and encourage them
