I never tried this with the alternative position, but in principle you can influence the coordinates the printer uses via GCode commands. So what I would try is: Mount the toolhead with the alternative holes, then move the left nozzle to the desired 0,0,0 position, i.e. nozzle touches the printbed at the left front corner, and then issue
G92 X0 Y0 Z0
This tells the printer that it should use a coordinate system that has its origin at the position you have chosen.
Things you would need to test:
- does bed levelling preserve and respect this coordinate system? If not: Is bed levelling working by running the levelling first, and then do G92 at the desired position? (At least that should work, unless levelling gets confused by the high Z position of the toolhead…)
- Which coordinates can both nozzles reach? This will give you the limits of your build volume. It may be that the right nozzle is not able to reach the outer left of the print bed.
And please report back 
I planned to try this the moment I was in the need for more Z height, but as of now this never occured. Knowing it would work in principle would be great!
G92 in principle works, I used that to max out Y: Maximum Y Position 347mm? - #3 by Hauke