It does depend on the adjustment between the fence and the base of the crosscut. I typically use a large framing square that is known to be accurate. I apply the square against the fence and check the gap between the front of the saw blade and the back of the blade. The crosscut sled I use has an adjustable fence so it can be tuned to arrive at 90 degrees. The fence is attached with a pivot at one end closest to the kerf area and the other end has an adjustment mechanism to dial in the 90 degree angle.
So I would set it up to have a fine adjustment so you can accurately dial in the square setting. Also, ensure the miter slots are perfectly parallel to the saw blade. Measure front and back of the blade against the miter slot openings.
Norman
Norman Pirollo