How can I bolt a microwave to the upper cabinet if the bolt hole is stripped?
If the microwave is under warranty then get a replacement telling them it's a manufacturing defect, if not then you can do what you want with it so my course of action would be to remove the cover and see what my options are. The metal covers on microwaves are generally pretty easy to get off, a few screws and they slide off, getting them back on is the reverse process. Working with the cover on is challenging because you don't want metal shavings getting into the electronics or tools to damage it while you're working. 

I like your nut on the underside idea, it's simple and the least work once you have the cover off, unless you can borrow a tap and die set and re-cut the thread. You could try that with the cover on of course, however small shavings of metal will get into the microwave from that, which could lead to a short. Epoxy on the top is not a great course because it's probably painted, you'd be gluing onto the paint instead of metal, so you'd want to sand a clean surface if you tried that. It might hold or it might not, and if it were me I'd be constantly worried it was going to drop on me. 

There are other options, for instance a toggle bolt:



If you can find one of these that's small enough to fit through the hole, and if there's enough space behind the hold you could push one it through and use it to hold it up, just be aware you wouldn't be able to get it back out again without taking the cover off. Personally I'd use that as a last option, my first would be to get the cover off, just be careful about your own safety around the electronics.