I am wondering if you could have possibly gotten the message wrong. You definitely don't want to braze any patch panels on with a torch and flux coated rods. That said, you can, but you have to be sure to clean, grind, brush or knock every trace of the flux off before any body filler or finishing process is done. If not, you will have future bubbling problems for sure.
The flux core wire for a MIG doesn't seem to pose that same problem though.