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There is a specific microwave interior cavity paint which is used to paint microwave, below is a link to where you can buy a can.
CLICK HERE for cavity paint.
Now as for the low spots, that might be something you have to just deal with. Sand down the rusted spots and paint over it. There isn't a filler that I know which will work. If you wanted to try to fill a hole you'd probably have to weld metal and grind it down and such---this is not a practice used to repair microwaves typically. Usually if you can sand it and paint it then great. If the rust goes all the way through, the microwave is considered un-repairable and the manufacture states to replace the microwave.
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