Which microwave brand and model have you found? If you have found one that you like read the installation and specifications for it at the manufacturer's website. These should tell you whether they have a trim kit for it, and the mandatory clearances needed for the model you chose. Most trim kits simply come shy of the outer cabinet of the microwave so a portion of the front can be protruding through the kit, but this should all be listed in the installation and specifications. Also remember that your microwave probably has feet so check the specifications to see where they are located to establish that they are not past or resting on the trim kit.

If your mounting on a partition wall (not load bearing)----you can hve the studs cut out which picks up about 4" of extra depth---that way--you don't have to have such a deep cabinet

This would apply to having the micro in a wall cab---with open counter below. I am planning this----so I will only need a 16" deep cabinet for the micro---leaving plenty of usable counter space below