I'm absolutely no familiar with Atari ST hardware, but the floppy drive implementation should be similar to the solution used in the case of Enterprise 128. This computer was a commercial failure everywhere, but very popular in Hungary, as it gave a relative powerful hardware for a low price. The EP's floppy controller contained a WD1772 IC with enhanced data separator, and was able to write not only 9, but 10 or even 11 sectors to one track. And besides it was possible to add extra tracks to the disk, the 'Hungarian Standard' was 840kB (84 tracks/10 sectors - 11 sectors were sometimes unreliable), but in theory the maximum was 990kB on a standard DS/DD disk (90 tracks, 11 sectors). And the same for 5,25" drives!!!
I found a nice description about it, sorry, it's in Hungarian, but Google translate may help..:http://ep128.hu/Ep_Hardware/PC_FDD.htm