My 92 LY had similar damage so I understand where you're coming from. Personally I see no reason to do the interior calk to the frame but I don't see any issue with it either. I would bond the new boards directly to the outside fiberglass using your glue of choice (I used Gorilla Glue). Make sure that the surface is clean and clear of any deteriorated material.
As for the screws, you can screw through the fiberglass, but the big thing is to give that metal striping a sold material to bite into. It's that striping that covers the sealant and clamps the top end cap to the sides. I wouldn't use any screw locations that would penetrate the sides but not go through the calking material.
The material used to seal the seam is a butyl rubber tape. It looks like this:
Usually comes in 20 or 50' rolls and is pretty cheap. It comes in gray and black. Get it wide enough to cover the seam behind the metal strip and overlap each side by a little. Usually 3/4 or 1" wide is what I get. This stuff is great for around windows too. Just about anyplace that needs to be sealed and is clamped in place. Don't be too worried about any material that squishes out. Just use a X-acto knife or razor blade and cut the excess off once the metal strip screwed down.
The stuff is cheap and you can buy it online or any RV place. Camping world carries it and it's on sale: Butyl Tape 3/4"x30' - Dicor BT-1834-1 - Installation Tools & Supplies - Camping World
Here's a another place I've used:Butyl Rubber Tape - Flexible tacky adhesive Sealing Tape - PPL Motor Homes