Yes, there are probably non-trivial pressure imbalances on the sides, but since the ball is rifled these imbalances rotate so that when averaged over a rotation, the imbalances would cancel.
I'm interested in the change of orientation of a football as it travels through the air
Really quickly, I'm going to define a reference frame as such:
x-axis: from one touchdown to the other, and in this case, also the line from quarterback to receiver.
y: along the turf from sideline to...