I use the Qwas dogs to align the guide rail parallel to one column of holes. The I use Qwas dogs to align the fence to one row of holes. By definition, the fence and the rail are now square to each other. In practice, this gets it closer to square then you can extract precision from the rail. It you've never done it, pick the rail up and put it back down 10 times, using feeler gauges to determine exactly how out of square the rail is. Then do this same test with the rail flat on the table, with the rail at the height for 3/4 sheet goods, at the height for 4/4 lumber, and at the height for 8/4 lumber. You'll be surprised how much scatter there is at any one given height and the amount that it can change with height is quite an eye opener.
The precision and accuracy of the MFT rail and fence is very good for a quite easily portable worksite tool. However, to get that last gasp of precision and accuracy, it's not as much of a no-brainer as a crosscut sled.