Are you saying that the bed of your lathe is out of line with the spindle.
If not, I take it that the table is an independent piece of machinery that sits on the original lathe bed, but it is out of square and you cannot correct it. Does this provide vertical movement so you can use your spindle to mill pieces with ??
Either way, I think it would be very difficult for Mach Turn to provide an instant solution "on the move" so to speak. The offset to be provided would depend on the distance travelled, but then if you are applying this on an out of square axis, then another allowance would be needed. If you were turning on an out of square axis, then for every 1 inch of movement on the axis you would get the cosine of the angle movement in the tool.
The only thing I can think of in a simple way is to increase the number of pulses per inch on the stepper motor drivers to compensate for the shortfall. The only problem with this is, you could correct one axis this way, but the tool would also move marginally on the other axis and I cannot think of a way to rectifiy that.
The real alternative that I have just thought of is to write a VB script to put in the compensation automaticall to compensate and this would be relatively easy for say code g0 and g1, but how complicated they would be for g2 and g3 for example, I shudder to think.