You can assign the 2x additional foot switches to pretty much any CC message that you wish (i.e. CC01/Modulation or Aftertouch) - then from that, it depends very much on the MFX as to which aspects you can control.
CC01/Mod by default controls the rotary MFX for the organs, so you can control rotary speed with that (Slow/fast - not variable), but it's not actually disengaging the MFX of the Rotary effect. You can also assign to the brake control.
So, NO to disabling MFX altogether, but Yes to being able to control the brake/speed of the rotary - Disabling the MFX altogether would cause a drop in volume, as it's a speaker sim too, so brake/speed is preferred imo.
As for drum patterns? how do you mean with that? You can start/stop the sequencer with a foot pedal, but that's the only real control i could think you have with drum patterns - i think the only way to select which drum patterns are playing is by the screen/buttons.
Drum (snare) rolls you can by assigning foot pedal to CC01/Mod, once again, The supernatural kits will roll depending on the amount of expression given.
However, i'm wondering if you're confusing the FA with an arranger keyboard and when you mention 'rolls' you actually mean fills, and are wanting to use the FA as an arranger firing off drum patterns/fills?
If so, the FA is not suited for that kind of use, it's more workstation in that tracks are best recorded one-by-one in the sequencer.
As a comparison, something like the Yamaha MOXF are much stronger in the arrangement area, particularly in regards to auto-accompiants/arps etc. But then, that's always been their thing.
