Why not weld the stainless nuts to a stainless backing plate and glass that to the inside of the
hull. The nuts would need fairly big washers anyway to spread the compressive loading on the
hull material. The bolts go through the exterior
chain plate, through the hull and into the captive nuts. You don't need access to the nuts at all.
Your idea of using a machine screw with a round head and recessed hex key slot is good as that will not chew up fenders (and other boats' topsides) as much as a standard hex head bolt. Will also look less "agricultural".