I was at my boat earlier today before I saw your question, but I did take a look at things again. It looked like I might be able to at least reach the inboard floor drain portion of the scuppers. I did not try to reach the outlet portion of the hose, nor did I try to reach the outboard floor drain. Not sure if I could reach that or not, but even if I could It did not look like it would be fun to do. However, it did look like it would be pretty easy to cut away a portion of the vertical plywood on the starboard outside of the rear compartment, to gain access to everything. You still might have to be a bit of a contortionist to complete the job, but I think visibility would be pretty good. I think I would feel comfortable doing that and I don't think it would be a problem patching it up with some cloth and resin and there would not be any issue of additional water intrusion.
I'm sure that you could do the job by cutting another six inch access hole near the scuppers and put a pop out plate in to cover it up, and I believe things would work out fine for you. That said, I have not had my boat that long and I've already replaced the gaskets for the three floor plates that were factory installed. That is a concern for me, but maybe I'm just being anal. I have yet to remove the two large floor panels, but I plan on doing that this winter to check the tanks and everything else that is under the floor. Maybe I should wait until I do that before I finalize my thoughts.
Anyway, I hope that helps and I look forward to hearing how you finally address this issue.