Part of the issue is that while USB and 3 1/2" floppies overlapped for some time, the 5 1/4" floppy was already long dead by the time USB was introduced. I wouldn't be surprised if the 3 1/2" USB floppy drives you buy today are basically the same design developed in the late 90s. They're so cheap because they've been made the same way for decades now.
The 5 1/4 USB drive is bespoke hardware, which is why it is so expensive. I'd imagine it has a more software described interface so it can handle the galaxy of incompatible sectoring and formatting standards used by different companies back in the day. It used to be that if you formatted a floppy on one computer it was not likely to work on any other brand of computers. Having the formatting details be in software/firmware would make the drive far more useful for historians.