It's my contention that all manufacture's or designer's would like to see the boat become 1 piece.
This is not the case as it's just not easy to do and costly in production work.
I did it the hard way, but it's a brick house. I did it all the way around the boat from the outside. There is a lot of fairing to get it right again. 1808 and a layer of 3/4oz mat was vacuum bagged. I filled the gap with 5200 first, let it setup for over a week and then removed the pop rivit's. Then did the glass work.
This is just one section being done.
As to removing the screw's and replacing with machine screw's. I didn't see this brought out anywhere, but I would just R&R a few at a time so the cap doesn't shift.