As long as all the ingredients for the item are in the bag, the items will be made in the bag. The tools don't have to be in the bag.
If you're using the in-game salvage bag (which is infinitely better than the UOA recycle agent), try setting up the organizer agent to move ingots/leather/cloth into the salvage bag, by making it one of you organizing bags. I'm not sure if there is the ability to invoke organizer agent as part of a macro, but even without it, that's only one extra keystroke.