Mitsu/Getrag will be very cost conscious so if they are explicitly asking for people to upgrade to the 2009 firmware to do the teach-in and then back to 2008 afterwards then you can be sure that there is a reason for it rather than just to waste everyone's time (and indeed Mitsu's own money if the work is being done under warranty). It's pretty clear that there are three different hardware revisions of the SST/mechatronic unit so it makes sense that they should have different firmwares to accommodate the differences.
The "5th gear cold start test" is a diagnostic test that the SST performs when the car is started from cold where it briefly engages 5th gear slightly causing the car to step forward against the handbrake/parking brake. Apart from the forward movement it results in various noises (clunks/thuds) and for some people occasionally a gearbox crunch so Mitsu/Getrag seemingly removed the test as people were bringing cars to dealerships saying the gearbox was dying.
It's not so much the gearbox response in normal mode that I have an issue with it's the throttle response on the accelerator pedal in that mode that makes it so poor. Normal is more like a standard automatic set up where you have to push the pedal much further whereas I prefer sport mode as the pedal is more sensitive like a manual car.