I've done tons of body work on proton packs, from filling holes to basically rebuilding a torn vaccuform shell from scratch
For holes, I've used epoxy putty for plastic (J-B Weld PlasicWeld Expoxy Putty)
It's like a stick of putty that has an inner layer and outer layer. You slice off a little piece with a razor, and then kneed the putty together to combine both layers and "activate" it. I've used it to plug screw holes and join minor parts together. I dries insanely rock hard and it's sandable (Although it's a little tough to sand)
I've had better luck with regular Bondo auto body filler, which is a 2 part filler. It dries hard with just a little flex and is sandable. Downside of this is it has very strong smell, and you have to apply with a scraper (It's like the texture and consistency of cake frosting)
For small cracks some people use Bondo Glazing and Spot Putty, but it's really only good for smoothing surface imperfections and dries bright red which can be problematic if paint chips.
Out of all of these I prefer the Bondo Auto Body filler, but i've used combinations of all 3 in certain circumstances.
1: Epoxy Putty - Fill Large Gaps and Holes (Just below the surface to be sanded, usually from behind on the inside of the pack)
2: Bondo Auto Body Filler - Apply to Surface of Epoxy putty filled area and sand flush
3: Bondo Spot Putty, smooth out any imperfections
Edit: You are bringing back horrifying flashbacks of when my buddy challenged me to repair his vaccuform shell that looked like it got ran over by a car and had gaping holes.... I'll never do that again but I Gotta share these.