Does OTR Microwave need to be flush against upper cabinet?
Yes there is normally a gap between the OTR and the cabinet above it.  If you review the install instructions usually the gap is 1".  

The gap is almost required and the typically U shaped metal mount on the back wall requires that the OTR be tilted in to be installed.  The tilting then requires that both the air output and the electrical cord coming out of the top of the unit thread into receiving holes in the bottom of the upper cabinet.  When tilting if you were to make it flush you'd need a trench type hole to allow the electrical cord to feed up into the upper cabinet.  I've done it flush before but it was quite a bit more difficult and the lower shelf of the cabinet above had to be butchered.