Hi Greig,
I'm not sure how you are accustomed to working, but I always use an appropriate Gcode to define the tool's position relative to to the part datum. In particular I use a G92 command but this may not be what you would use. This does require actual editing of the code.
It sounds like you want to make a movement outside of the work coordinate system. However, it seems to me that you could get yourself in a lot of trouble doing this because on the next work offset, you would still be carrying the error of your previous mdi movement. Sounds like a recipe for scrap I may not be understanding what you are saying though.