I hope I'm able to explain this clearly... I'll try.
It is first and perhaps foremost that there are no points where the sheet metal must be "forced" into position. You know, pulling, pushing, etc. to get a bolt in. NO, NEVER.
Okay, the inner pans... they only fit to the fenders one way. I'm always certain they attach to the fender (again) with no force applied. This often means I must elongate a hole or two or more.
If you attempt to install the pan to the frame / body first, then you are left with attempting to make the fender not only align with the pan, but the body as well. Kind of introducing yet another hurdle.
Moving ahead with the front metal installation...when I install each fender, they too must not be forced. I do not recall a single time when I did not have to elongate holes.
Keep in mind, I'm kind of a "nut" when it comes to perfect alignment. I'd seen too many otherwise nice restorations with the hoods askew, etc.
To me that's akin to baking a perfect cake and slopping on the frosting.
Oh, one other thing that goes directly to your inquiry... much easier to install the inner pan to each fender while on the bench than while the inner pan is installed.
Don't forget that strip of anti-squeak material that must be installed between the pan and fender.