If you've looked at my CPLD source code, the internal floppy disk registers and their meanings are described in a big comment table, right at the top of the file: no reverse-engineering necessary. It's basically the same set of registers, whether it's the Sony 400K, 800K, or 1440K mechanism. The registers are used to do things like turn the drive motor on, step one track in or out, measure the drive's rotation speed, and read data from a track. And yes, these are not the same thing as the IWM or SWIM's registers.

The internal floppy disk registers are also described in this developer doc from m68k-linux, which refers to them as "Disk Drive Status and Control Bits. Scroll down to the paragraph that begins "In addition to programming the IWM, it is also necessary to program the drive itself": http://www.mac.linux-m68k.org/devel/iwm.php