Captive nuts are just that. Assemble everything on the seat pan, then just tack weld the nuts in place. Everything will fit as you have fixed the nuts in their final all tightened up position.
Car exhaust mountings, the sort with two threaded studs bonded to a rubber block ("cotton reels") make a handy and compliant rear seat mount, and a custom mount from the frame will be a better way to support the seat pan, avoiding extra load on the relatively weak rear mudguard. The original design, as always, is a compromise between the designer, production engineers and cost accountants......
Swarfy.