I don't think the bottom of an smc hull is the best place for bondo. It might work but it will be a mechanical bond only because it's polyester based and bondo loves to absorb water when it's exposed.
Indeed, but any filler is a mechanical bond on the bottom of the ski. The only way to get a chemical bond is monolithic curing, and that SMC hull has long since cured. Epoxy with a faring filler will also get rubbed about pretty quickly once the paint wears of - so the only permanent fix is epoxy + cabosil which is a pain to finish.
So, my vote is do it cheap, paint it with a hard paint, and then do it again when it wears off. Or maybe you learn your lesson the second time around and just leave it :sneaky: