I know this post was semi tongue in cheek, but it also underscores the importance of having a good architect and a good relationship with said architect during a residential project.
Ive fought with numerous electricians specifically and other trades less frequently because home building is more a science in bio-physics, human physiology and psychology than it is a study in Construction Science. Once code and best practices are met, then there is huge room, or should be, for personal preference. Especially if this is your forever home and not an investment. I wont go into my personal pet peeves so as to not de-rail the thread, but regarding the issue (microwave) at hand.
When we remodeled our kitchen, 7ish years ago, I went with an undercounter microwave. Our contractor had A&E in house and they gave me all the reasons. I am pretty sure I even discussed this with you and/or Cyd. It all made perfect logical sense. After 6 months I spent almost $3k redesigning our kitchen and cabinet layout just to get rid of that microwave. Anyone who know how cheap I am understands what a huge issue this had to be for me. Simply put we hated bending down to put crap in the microwave and hated more bending down to clean the microwave. Around my house ovens get cleaned 2-3x a year by the self clean and 1x a year by hand. In contrast with 2 teens the microwave gets cleaned weekly where a kid cooks a hot pocket too long or that sauce bubble popped or whatever. And that was a weekly session of down on the knees scrubbing. We hated it. Sure it was the logical right answer...and we hated our prior over oven microwave/hood duct combo...but found for our lifestlye and preferences we could deal with a less than ideal duct better than an ideal microwave.
All the other stuff is true. Last week at Thanksgiving it was a clutter funnel...but Ill deal with that 2-3x a year before a weekly kneeling to clean. Now we decied to get a tad creative and have a 22" deep micro above the stove. I'm not sure the installation meets perfect code (picture frame recessed into the wall - front flush with cabinets) but it works, is safe and secure. The one complaint, again rare, is if we are cooking something very smokey the micro/hood combo just cant exhaust the smoke as well. I learned how to bake bacon and its better than you would ever guess....in fact Id say better than pan fried.
But in short, if your architect isnt listening to his client, on non code compliant issues, fire him. Immediately.