I don't think either of these scenarios is likely. I've never heard of a lizard being put in a snake bag for transport...they usually go in little plastic cups with lids. I can't imagine that any reasonable businessman would intentionally put a baby lizard into a bag...much less a bag with snakes in it. I'm very glad he wasn't hurt in the journey!
Seems most likely to me that he escaped from some other table and was hiding in that bag that your snakes got put into. Beautiful snakes, btw!And frilled dragons are awesome creatures...I'm glad you're deciding to keep it...I hope we can see pics of it as it grows!