Let's say you have standard flute body and a heavy wall flute body. Both bodies are of the same brand, are handmade, same model, and have the exact same specifications. The only difference between the two is that one is .015 tubing and the other is .017. Now, let's say you try ONE single headjoint on both flute bodies.

My question: Will the .017 flute body always make the flute more resistant, or is it possible that the standard wall flute may be more resistant. In short... Does heavy wall always equal more resistance?

If they are the same model then yes, heavy wall usually is more resistant. To each his own though and it may vary from player to player. If you get a chance to try each one the best thing to do would be make your own judgment on it and see what you like.