Whether the back of the jig is square to the blade or not is irrelevant.

If you want the newly cut edge to be square to the old edge that is resting against the jig's back, then the back of the fence must be square to the track, not to the blade. This is because the jig slides in the track.

If the blade is not parallel to the track, then either it angles away from the cut, which will probably cause a rough edge or maybe even some binding, or it angles into the cut, which would definitely cause binding and would be dangerous.

I am not an experienced craftsman, so I am certainly open to disagreement, but it sure seems to me that if your blade is not parallel to the track, then you have a serious problem.