I guess using the 765a makes the software a lot simpler (it just requests data at a particular location) but means it's much more limited because of it.
The Amiga I believe is basically just Paula chucking out bits which then have to get decoded, isn't it? I.e. great for copy protection, not so great for ease of use (hence Kickstart routines).
The PC was built from off the shelf parts and the upd765a was basically all that was available, you can make an argument for sector gaps or a track gap but what was available to them had sector gaps so it wasn't really a choice.
The Amiga had a better price/performance ratio because everything as custom and having a track gap is easier from the hardware point of view, so it was cheaper for them to design and build. The greater storage space was a side effect of that, I doubt they ever considered doing it any other way.
trackdisk.device would have existed no matter how the hardware worked though. Even on the PC you wouldn't talk directly to the floppy controller. The only real difference is that the Amiga generally uses the same code for booting from a floppy and once the operating system is loaded. While on the PC you have separate device drivers. Both ways have their merits.