I am posting as an additional data point. Use the information as you see fit.
I drilled the glass and roll bar per instructions. That is, with the plexiglass clecoed to the roll bar and tapped through the plexiglass and the roll bar. Made it through 3 or 4. 5, not so much. The tap broke off in the roll bar. Now I have a broken tap half way through the plexiglass holding it firmly to the roll bar. Well, as one might surmise, I cracked the plexiglass. $700 and several weeks later I had a new plexiglass shipped to me from Vans.
So, from my experience, I suggest you NOT tap the roll bar while the plexiglass is on. Maybe you are better at it than I am but I don’t really see much advantage, and a great amount of risk, by having the plexiglass on while tapping. On the new plexiglass I tapped all the holes on the roll bar without having the plexiglass on. It worked just fine.
As is most other details in the construction manual, the instruction to tap through the holes in the plexi window is for a very specific reason based on a lot of experience working with builders
To put it bluntly, tapping a hole in aluminum is something that a large percentage of builders don’t seem to be able to do.
You admitted yourself that you broke a tap after only four holes.
6–32 taps are somewhat fragile, but if somebody is doing this process with some proper instruction and practice, a broken tap should not happen.
For some extra insurance, don’t ever use cheapo three or four flute taps from a hardware store. Get a high-quality to flute tap from someplace like MSC or similar.
Anyway, the problem that is being solved by tapping through the window, is that the hole actually gets tapped with proper alignment. Now this is assuming that when the holes were originally drilled, the instructions were followed.
The window helps maintain alignment of the tap.
I think there has been way more windows cracked from people trying to install screws during window installation, into holes that were tapped crooked.
The bottom line is that there is no process that will 100% prevent people from getting a negative result when they are using poor technique, but tapping through the window was found to be a way that greatly improved the odds of success, even if it doesn’t work 100% of the time for 100% of the builders.