The rationale: The rules as written are simple and elegant, but don't allow for the end product to have both good qualities and bad qualities from the results spending chart. I also lamented the fact that there isn't otherwise a way to be sure what the end product is going to be, as far as extra qualities or stats go.
I read the crafting rules the way you did initially as well, but you need to read them again. They do allow for both good and bad results. Unlike most checks, you do not cancel advantage and threat. You spend both.
No, you still make a standard roll and use the end results.
On Page 75 of Special Modifications under the steps for construction it instructs the player to make a check to see if they can craft the item. It then instructs for the player to first spend advantage and triumph, followed by the GM spending threat and despair. As it makes no mention of cancelling advantage or threat, I can see how this could be read both ways. I personally do not cancel the results allowing for both positive and negative traits in an item, I also believe that this is the simplest solution.
PCs spend Advantages and Triumphs by default and GMs spend Threat and Despair by default. They aren't going to reprint all of the dice mechanics rules every time they release a supplement with a new rule, however common sense would tell someone if they were going to flip the entire dice mechanic system on its head just for crafting they might jot a sentence down saying that. The dev answered sticky thread is replete with examples of assuming you can do something because it isn't written you can't is not correct.