So the reasoning behind your theory that "mtb pedals are more comfortable" stems from the fact that you tried some, and the road shoes were uncomfortable. Well I'm sorry but I don't think that's a very impartial test at all.
I don't think having road shoes and road pedals for commuting is going to cause me any significant problems, and it might give advantages which are significant enough for me to like, so I'm going to give it a try. I don't know what road shoes I want to get yet but don't want to spend a lot, I might have a look in decathlon, don't normally rate them but don't really see how they can go far wrong with shoes, as long as I can try them on and they're comfy.
FWIW the rest of the solution involves:
put the time atacs on the MTB and try and flog the PDM424s, M520s and probably also the V12s on
ebay. I've contacted specialized to try and get a replacement cleat bolt plate and had an email back from them saying they don't keep them but he would 'keep an eye out' for one for me. If one doesn't come in a few weeks then I'll go to a metalwork fabricators with the other one and ask them to replicate it. Can't be hard, probably won't cost more than a fiver.