I am not glassing the bases into place, I am glassing the aluminum into place. Then the bases will screw fasten to to the aluminum. Where I am glassing the brackets is not on the hull but on the floor. The reason I am not screwing it to the floor is I dont want to penetrate the floor and allow water to get to the wood and sencond I dont know how thick the floor is right there. I would be really pissed if I screwed into the hull.....
If I may be so bold, If I were you, I would prime the bare aluminum with some zinc based primer, it used to be a perfect job for zinc chromate, but hard to find these days...Aluminum oxidizes at a horrendous rate and I think if you are going to attach glass directly to the aluminum, you may have issues...
Another thought might be to just glass some hardwood blocks to the floor an bolt to those, fiberglass resin does not stick too well to bare aluminum...The blocks might be less work...I do totally agree with not wanting to drill through a good floor, if you do, seal the holes up very well with a marine grade caulk, not silicone.

Another little tidbit, make sure the aluminum is really rough before priming it so there is more surface area for the resin to soak in to...
Project looks badass, never though of using composites before....

GT