Keeping in mind that I'm a newbee, and this may not be a great idea, it goes like this;
Take a situation of a machine that has two basic setups that are vastly different; one is normal full table travel for general work and one has a 4th axis rig that takes up almost half of the table (of a baby mill).
My combination homing/limit switches are on a phono jack that just plugs into my CNC controller box. I think it would be a simple matter to add another switch in a position appropriate for the 4th axis work envelope, chain those together on a separate plug and have a second XML file for 4th axis projects. The xml could have the approproate limits for the 4th axis envelope and any other changes that may benafit that type of work.
So as a part of the 4th axis setup, I simply put the rig on the table, plug in the appropriate limit/homing switch chain into the CNC controller and start Mach with the 4th axis XML. Now I have fast homing and limits appropriate for the 4th axis envelope.
Maybe I'm missing something, but this seems like a very usefull proceedure.