Misalignment of the door leaf and door frame is a common issue. In terms of requirement of the installation to comply with product certification the door leaf must not stand proud of the door frame or if this is permitted there will be a very tight allowance, typically 1mm.
As far as the door leaf being "off" the rebate stop, I have not yet encountered a limit for this issue and recommend where the stop is the planted type that it be moved to compensate for any twist in the door. For a frame with a rebate machined from the solid this would not be possible of course. To be correct, one should always check with the particular door manufacturer to see what is permitted in terms of tolerance for the door leaf to stop dimension.