If you think about it. they were mapped to the buttons that are hardest to use, 1,2,3 are I found easy-ish to press whenever. 4,6 though many games didn't have them for strafing, Its ok cause if I did get a pro controller (Which I really want but am not going to spend $80) I would probably put my most used weapon in IS (The Gatling gun) on the 4, or 6 spot, for a fast weapon change.
7,8,9 are not often used as far to my knowledge and even is IS they are only the rifle or chainsaw, and the fist...
from what I know of there are SNES, and Megadrive programmable pads or something, they use an odd system for extra buttons (but so useful when wanting a button to do a hadouken)
and the Jaguar's standard controllers are really hollow. They could probably have made it like that, with the controller costing maybe back then $10 more, though Im not 100% sure.
They really couldn't have ingame options of changing it cause it would not match the overlay, and the pro controller wasn't made yet! If the makers knew about it I have no doubt they make the controls fit well into it, but they most likely wanted to make the buttons easy to press so they were going all button combos, and first numbers.