Obviously it is your car and if you want to keep the vinyl that is your decision, I had a half vinyl on my Monte and I removed it and welded up the holes and I bought the rear filler panel and quarter windows off a hardtop.Not likely. Plus I'm doing all the prep work short of stretching the actual vinyl. And there wouldn't be any worry of rust appearing with proper prep and regular washings.
If you decided to remove the vinyl a simple HF welder will get the job done and it doesn't take that much skill to weld up 1/8" holes and there are plenty of beginner welding videos out there.
I like my cars to be aggressive and sporty looking and IMO a vinyl takes away from that look (imagine my Monte with a vinyl now) so if that is not the vision you have for your car then carry on.