Some more details which I found out two years ago when working on the fix: The TI system allows for industry floppy drives, no special devices from TI, just the controllers. Earlier controllers (with wd17xx) only allow 40 tracks, later controllers (smc92x4) also allowed for 80 track drives. Instead of doing a test seek, the creator of the advanced controller decided to make use of dip switches to inform the controller about the number of physical tracks of the attached drive.
This observation suggests that the TI99 drives should be devices with their own PORT_DIPSETTING entry: is this something possible with the actual core? Do the "Dipswitches" and "Configuration" menu allow sub-menus?