@Jmod86, I have felt your pain, and although they're not all jumping out of the woodwork to comment, I'd bet that the rest of the forum members have also.
If I were in your position, the first thing that I would do is have Glastron explain to you why the issue is not a problem in terms of long term structural reliability and further cosmetic degradation, in detail, and in writing. If their formal response makes sense to you, this will be useful to have when you sell the boat. If it does not make sense to you, then the ball is in your court to seek an assessment from a qualified marine fiberglass repair shop who is approved by Glastron for warranty repair work (not the dealer that you've been working with). When you bring your boat to them, do not do it on the basis of a warranty repair. Do this independently of Glastron. Bring it to them for their assessment with the understanding that you'll pay for the repair. I know that this takes up your time, but it will enable you to get a clear view of the situation.
You're lucky in that the problem can be inspected without significant labor investment.
To make you feel better, when I first purchased my boat, after striking out with the dealer that I purchased the boat from, I approached another dealer to get some leaks fixed, but because the root cause analysis phase was labor intensive, I had to agree to pay, in case Yamaha did not step up, even before the new dealership would touch the boat. I got the sense that they've been burned in the past where they spent days looking for something to fix that will stop the leak and they never found it, so no repair = no reimbursement from Yamaha.
Is there a way that you can determine whether water is leaking into the boat from this spot?