I don't think I'd use Bondo for a trap-out as it continues to outgas toxic fumes for some time during and after drying. Definitely toxic to humans, don't know about bees. Because the drying time is longer than silicone, I'd be worried about poisoning the bees in the cavity if the drying byproducts are bee-toxic.
Might work better for filling the hollow, but such a large volume of the stuff would take an awfully long time to dry (and be more expensive than alternatives). Expanding foam (Great Stuff) won't work for a trapout because the bees can chew through it, but it should work to fill the hollow afterwards because the goal is just to make the site unattractive for future swarms to settle in.