The bitrate should make no perceptible difference whatsoever, but the Space setting, yes.
The 96kHz option is simply the standard 44.1kHz output upsampled, the point being one of convenience when running one's DAW at 96kHz.
I A/B'ed the bitrates several times and to my ears they really made a difference. Not saying I might not have imagined it or played the guitar slightly different each time but I was sure enough to leave it on 99khz. Maybe it has to do with how my Focusrite receives the data, not sure.