kevint,
If you coat with etch primer, then sand through the primer (accidentally) when roughing for bondo, you are back to square one with no bare metal protection. I don't think you are suppose to apply etch primer OVER bondo.
If you etch prime, then coat with a 2k primer, your finish is solid, and you merely rough the 2k a tad for bondo...no sand through problems. You can then spot coat over your bondo with 2k again.
This is how I understand it.
Stuart