Some large or home built machines need to be able to compensate for inaccuracies in the machine frame. Some motion control cards have this function - eg DeltaTau PMAC.
You already have screw mapping which is a similar function so I would assume it wouldn't be hard to implement this.
Our machines are about 12 metres long welded structures similar to a lathe. The PMAC takes care of the inaccuracies in the frame.