Re: bondo and gelcoat
In place of bondo type fillers, regular poly resin can be mixed with thickening fibers and/or milled fiberglass to make a putty that will not absorb water. Use it to fill the void and gel coat over it.
Complaints of auto filler used on boats comes from most auto filler containing talc, which is reported to absorb water over time. Personally, I have never seen it happen, on a car or on a boat.
Like with anything else, proper prep will give the best results.
Another thickener you might find in the hardware store is wood flour. Used to thicken resin. I have used plain old cooking flour (a tip I got from the wood boat building forums) to thicken poly and epoxy. Both are holding up as good as any other thickener. Mix up two oz of resin and mix with flour and see what a great thickener it really is.
BTW, a half pound of commercial thickener and another of milled glass will last a very long time for repairs, and is very cheap, and being light, is cheap to ship too.