The bolt hole tolerances on those plates allow enough movement that they are not likely to be perfectly aligned with each other. One of my only complaints about the machine is that there is no way to easily check that the X axis tube is square to the Y axis, because there is too much stuff in the way to use a square. If you want to adjust the X-axis tube, you need to loosen the 6 bolts that attach it to the bearing blocks and turn one of the lead screws by hand, so it touches on both sides and then tighten the 6 bolts again.