Apparently the holes in the MFT/3 top are CNC'd so the holes should be square to each other, i.e. a "horizontal" row of holes (left to right) should be 90 degrees to a "vertical" column of holes (front to back). Therefore, when indexing off the qwas dogs, the horizontal dogs and vertical dogs should measures square.
However, the rail is set off the frame of the table, it is not attached to the perforated top. Therefore, if the perforated top was not exactly square in the CNC machine when made, or not attached exactly square to the frame of the MFT/3, the row of holes in the perforated top, although straight, would not be exactly parallel to the edge of the table. Mine is also off very slightly.
Therefore, when you set the fence alignment using the qwas dogs, and the rail alignment via the table frame, they are being indexed off two independent parts, thus are not automatically at 90 degrees to each other. You can certainly set the fence position using the qwas dogs for convenience as this alignment with the edge of the table will always be consistent even if not exactly parallel, but then align the rail position by using a square aligned to the actual fence rather than to a qwas dog on the top.
Obviously, if your top is in perfect alignment, you can just use the dogs. Just don't take it for granted, check first.
A second issue is slop between the rail and the positioner it is lowered into, but this slop (if it was occurring) would likely be fairly obvious. Solutions for the slop have been addressed elsewhere on FOG.