Griz, its like DerekJ said, mostly to get the panel gaps and alignment correct. But also to redo some things in the engine compartment, remove the fender beads, etc. I had spent hours fitting the panels and doors to the car before I sent it in for body work, then removed everything again to take just the panels and doors back for paint, then reassemble every thing again, then remove them to do something I should have done before.....you get the picture. I know every screw and bolt on those panels very well.....
As far as the air tubing for the hearer and fresh air duct, I found it better to leave them off until I installed the front fenders. It's certainly easier to put them on before the fenders, but them you have an almost impossible job in getting the fender bolts on with them in place.
Oh by the way, you get to remove the doors every time you want the take the front fenders off. I finally cut the heads off 4 bolts that I would screw into the hinge mounting holes (two on the upper and two on the lower hinge) to use as guide pins when rehanging the doors. That way I didn't have to try to hold the door in position while I started the door hinge screws. Once I had two Phillip headed screws installed in each hinge, I pulled the "headless screws" and installed the Remaining PH screws. Saved a lot of frustration or asking my wife to help.