I never assume my mounting supplies are square; most of the time they are not, even expensive mat boards. Things like gator are even less likely to be square in my opinion. For my mounting boards (typically being sized from a stock 32x40 Rising board), my routine is to first trim about 1 inch from the long side in my mat cutter to get the first corner exactly square. From there I then rotate the board CCW and trim to size on each rotation. This way I'm pretty sure to get a sized board that is exactly square on each corner. Of course you must pay attention to seat the board in the mat cutter squarely against the extender arm, and it's worth making sure the arm is square to the line of cut as well.
I would recommend you size the mount board (gator in your case) BEFORE you mount anything to it.