You take it down, and replace with an actual hood. Easy. Then go buy a $99 one to put in the counter somewhere.

First, I would ask the builder if they can make the switch now, rather than you have to do it after the fact. Of course it will be an upcharge, but it might be worthwhile if the upcharge isn't too much. While the walls are open, I would ask the builder to have the exhaust duct that runs to the outside be 8" in diameter. Most builders install 6" or even 4" exhaust duct cause it's easier. But that means your exhaust will always be noisy and not efficient. The 8" diameter duct works much better.

If instead you have to make the switch yourself after moving in, there are a couple of things to be aware of. One of the disadvantages of an OTR MW is how close it is to the cooktop, making for a cramped feeling. In order to have the new hood fit properly under the cabinet where the MW was before, the hood needs to be 7-9" tall, not more. Any taller than that won't fit, as the hood will be too close to the cooktop. In addition, you will need to have extra backsplash tiles on hand when you make this switch. When you remove the OTR MW and replace with a hood, there will be uncovered wall behind the cooktop that you will need to add a couple rows of tiles to.

I saw a case where a person wanted to replace an OTR microwave with a hood. After removing the oven, he discovered that the backsplash reached only to the bottom of the oven, leaving a big gap between it and the new, shallower hood.