The gloss enamels are intended for use on glass, so I think they'll stay put especially after the triple thick. One thing to note is all subsequent touchups will sit on top of it rather than directly against the glass which creates a visible "bubble" of clear protectant in front of the paint even if it matches perfectly. It's not a big deal but it is noticeable under certain conditions.
Thus to consider...
1. Once you triple thick, you won't be able to cleanly razorblade your way back to the original paint layer because it will splinter all over the place. So plan accordingly because some areas might be better served by removing all of the original paint in a specific area first and then using gloss enamel as a fresh new layer of translucent color. I wish I had done this for the "GAME OVER" text... removed the flaky letters with an X-acto knife and painted in a replacement green color before doing the triple thick. Now I'll have to match what's there and touch it up.
2. The "clear bubble" isn't a big deal in my opinion. The only way to avoid it would be to do your touchups *before* triple thicking the glass. However... you had better be of LEGENDARY skill to attempt this because if you screw up there will be no way to recover short of razorblading the affected area and painting it all over from scratch. That's why triple thicking first is recommended... you can undo your mistakes with alcohol/water before they set.
I recommend triple thicking first & then doing touchups. Otherwise it's too easy to screw up. The movement of your brush near flaking paint might be enough to unseat it. Besides, "experimental technique #2" (globbing "white frost" onto the touchups) helps you match the opacity close to the original which looks great when backlit.
What sorts of long term issues are people running into with triple thick? Frankly I'm glad the stuff was available when I started this project because the flaking paint was already blowing away in the wind!