Protracker removes the lower border on the ST\STE.
If you were using a CRT there would be a Vertical Hold control which could adjust the position of the screen a bit.
There isn't usually such a control on LCDs.
Still got, still working: Atari 4Mb STe, 520STFM, 2.5Mb STF.
Hardware: Cumana CSA 354, Ultimate Ripper, Blitz Turbo, Synchro Express II (US and UK Versions).