Caulk tubes?
So you're asking about Bondo brand polyester resin, not Bondo the body filler? Originally, I thought you wanted to use the body filler, which isnt a good choice because of the talc as filler. Its also a polyester based product.
You pushed West System epoxy thru a hole drilled in a deck that has a rotten core material?
But only into the cavity between the 2 exterior layers of a cored deck?
Correct?
Bondo resin isnt a good substitute for epoxy. And I wouldnt count on the epoxy repairs you've already made being a long term solution. I doubt you removed all the effected core, and if theres any of it left behind, the problem will only migrate away from the areas you've filled w epoxy.