Can’t comment about the microwave (although if you are doing custom cabinetry, I don’t see why you couldn’t put your microwave wherever you found it convienient), but since you are “vertically challenged” (I am too btw), have you considered an oven with a Dutch door rather than the typical oven with a drop down door. Soooo much easier. I find that the door on the typical oven gets in my way and hits me in the chest or waist. With a Dutch door oven, there is nothing between you and an open oven ....much more convenient and safer too. They also have ovens with side opening doors (like on a microwave). Just a thought....

I do think having the micro under the counter would be awkward unless it was a microwave drawer. I would not want one with a swing door that low. But that’s me. Others have them and are fine with them.

Just realized you mentioned you wanted a convection microwave.....so no drawer possibilities I don’t think.

I wonder if it's not done that often simply because of visual balance. Usually the larger item is on the bottom. Having said that, if there is no other reason and it works for you, go for it.