As it is, good machines struggle to do 'perfect' circles. This will add another dimension of issues and tuning. I think its difficult enough to make a good machine work well and reliably if it is square (think of high speed machining), I cant see the value in taking something not square and then somehow mathematically trying to fix it.
Plus, not all errors are linear. If the X 'snakes' a few micron left and right, how would you compensate? You would need a massive calculation to know, your time is better spent just getting the mill square in the first place. Within reason, its not that difficult if you have the correct tools.
My own mill will probably have 0.05mm error only as I have a limitation on what tools / ability I have to do at home. But for me, that's fine.
Mostly, yes. But, most machines aren't great at moving near zero velocity, due to friction and backlash. So, lets say you are moving back and forth in the Y direction. The X will have to make very small moves with changing velocity direction, causing motion problems. These will be very small problems, but will likely show up as strange surface finish issues. If tiny surface finish issues are ok, then compensation will likely work for you.
nagging? its been a year, and I asked once. How is that nagging?