If done properly or even close to it, you are not going to thin the metal too much. I would be more concerned about the powder coating causing problems! Powdercoating or even the wrong paint can KEEP HEAT IN, that is NOT what you want from an oil pan.
Metal finishing or bondo (JB weld is not necessary) on a pan is no big deal. Unless of course you go over board and the article I posted explains it pretty well. You don't "grind" the metal to remove metal you do it to sort of "block" and see high and low spots like you do with a guide coat on plastic filler.
Brian
