After experimenting with various techniques using scrap plexiglass, I ended up using regular old three-flute cutters in a slow-turning electric drill to machine countersink the sliding portion of the canopy bubble. I countersunk slightly deeper than normal to leave room for the dimpled aluminum to "float" within the countersink as the plexiglass expands and contracts.
Doing all the holes took quite a while as I was going extra slow to try and avoid causing cracks. I still haven't drilled out any of the holes to make them oversize just yet. I also didn't touch the windshield yet, since I want to get the sliding canopy mostly done first.