When hard drives became common, it was no longer necessary to have two physical floppy drives, but it was often useful to swap disks, and so the same drive could be referred to as A: or B:—and MSDOS would prompt you to switch disks as necessary.
Also, I don’t think there ever was a convention for whether A: or B: was 3.5” or 5.25”. It probably depended on the manufacturer of the computer. On some of the machines I used, A: and B: were the same 5.25” drive, and the 3.5” drive was D:, for instance. And I can remember clones where A: was the 5.25” drive, and IBM machines where A: was the 3.5” drive.