Welcome to Fiberglass RV!
I think you've got a good idea with the bed rail. Rather than permanently mounting it, and then having to deal with the holes later, I'd probably cut a piece of plywood to match the front bunk configuration, and then mount the rail to the plywood, set the whole thing in place, and then put the cushion over it. The weight
of the plywood and your baby ought to keep the whole thing in place while in use.
Then, when you don't need it any more, it can just be pulled out and there's no holes to fill.
Camping with little ones can be challenging, and of course takes constant vigilance. I started both of my youngest camping when each was about month old. They both grew up doing it. It requires constant vigilance once they become toddlers, but the joy of discovery on their faces as they grow is priceless.
Have a ball and enjoy it all!