Does the pilot have an internal compass? If so, I don't think mounting it fore and aft would work.
1. The heading display, of it has one, would be 90deg off. Don't know if this would effect is operation.
2. When the pilot is mounted as intended, it pivots only a couple of degrees as it pushes the tiller back and forth. If you mount it fore and aft, I'm visualizing it pivoting a lot as it steers. That would confuse the compass and it might not be able to hold course. If the compass is remote, none of that would matter.
Lay everything out in the boat as you intend to install it, and compare the pilots position from fully retracted to fully extended. If its orientation relative to the center line changes much, that mounting won't work.