Yes - just to clarify, the calibration is done using maths i.e. if you know your threaded rod pitch (threads per inch or mm) you can convert this to lateral movement of the leadnut per motor step. The software takes care of the rest. Interestingly when I trialled mine I found the movement to be a smidge out, due to the inaccuracies in threaded rod manufacture (about 0.25% in my case). But it's easy to compensate for this by adjusting the steps per unit slightly. Using the Xylotex controller and metric M8 rod, the maths works out at 1260 motor steps per mm. This is the resolution of the machine (1/1260mm), however in reality the accuracy is considerably less than that due to backlash, wooden consturction and so on. Not bad though still
The hardware for the axes doesn't need to be identical, but I guess it simplifies things slightly if it is.
In terms of cutting a perfect rectangle, the other thing to watch out for is that the x and y axes are at exact right angles. Mine weren't, but you can check this easily by using the machine to make a mark in the four extreme corners of the movement range. If the diagonal measurements don't match, then the angle isn't 90 degrees and things need adjusting slightly to compensate.
Hope that helps