My experience is that if you have no contact to the check-in counter in BKK, then you don't pay. I.e. you have a transit in BKK and leave the transit area but you laready have your onward BP.

or has anyone ever been stopped by immigrations on the way back into transit to pay?

If you don't have your onward BP when arriving at BKK, you could try and get it from the transit desk and then just leave transit area...