What do I do if one or more Micro VGs ends up right on top of a rivet?

Look in the “note” section of the location drawing found in the back of the installation instructions for the official authorization to move the VG. You may move the Vortex Generator LATERALLY the shortest distance necessary to clear small obstacles, or you may file the foot of the vortex generator (leaving the blade intact) to fit over the rivet head.