Its possible going from A4 to MM6 to use LS1edit and simply turn off the DTCs related to A4, and tweak the tune and get away with it.
You would not be able to go from a MM6 to a A4 and do the same thing

BUT really the correct path is have someone who can do a GM flash, change 1 number in VIN so its seen a same car but with a MM6 and then flash the PCM with a TECH -II for that year/trannie.

Of course then you have to totally tune the new flash for your other mods but now things like the 1 to 4 cags, reverse lockout, how MM6 handles column lock and computes gear ratio is all functional with correct MM6 flash being used.

You will of course need a wiring loom that is for a MM6 rather then the A4 wiring it uses.

MM6 uses a clutch switch so you also need that functional.