Here an idea...

What causes the PCM to know something is bad with the transmission?
Faulty solenoids
faulty thermometer
faulty pressure sensor
....

What if I connect dummies (resistors and / or solenoids) to the A4 wires?
Will the PCM just "think" everything is fine because of the dummies and allow me to use the M6 troublefree?

OK this is a junkyard-mechanic idea, but why not?

Sure there is no reason you cannot measue the devices and see what their resistance is and then replace them with same value resistors but not sure if that neans much difference then turning the DTCs off

Not knowing a Trans am I do not know how much you have to also alter for if it has a column lock, lock for shifter, etc that a MM6 does not have

If still using a A4 PCM flash I would assume it looks to see if signals from shifter lock is there and is in park position so at the least you have to simulate that.

Whereas a MM6 has no shifter lock and only looks to see if clutch switch is open.

There is an helpful thread on another forum about modifying the electric system to make it work.
In reality it's not a clen job because the next owner will have an hard time if he brings the car in a garage.

I asked Carputing about reprogramming: apparently it's possible to load a M6 program keeping the old VIN. I'll post more about that when I'll exactly know how (and if) it really works.

Sure they can change the VIN # long enough to flash with a MM6 base and then just VIN back to real one.

Today I loaded the Carputing M6 program: it works!
Several parameters are now typical of a manual car: idle speed, trans oil temperature totally wrong, no tranny pressure, no commanded pressure...
Then I loaded the program back to the laptop: now it has my original VIN and the original calibration number!
At the end I loaded the A4 program (yes, I still have the automatic tranny) and everything went back to normal.

I don't know if this can be done using every program of the same year, I just know that Carputing did some modification to the program to fit my PCM.

Email me the 2 flashes and I will compare and verify that all MM6 functions are in fact correct

JR