In terms of what hardware will be changed when you do the MCU1 to MCU2 update, they will:
- Replace the physical MCU, so the processor that runs all the media interface/controls that drive the main screen and instrument panel, browser, climate control, etc. But this does not touch autopilot in any way as stated above
- Replace the center main screen
- Replace the screen for the instrument panel
- Remove the AM/FM/XM radio tuner - the original radio tuner is not compatible with the new MCU
- If selected as an addition upgrade item, install a new digital FM/XM radio tuner ... note there is NO option for AM with MCU2.
Hopefully you will see that all of your profiles will be carried over, although depending on how long the hold the car, some of these may need to download from cloud after you pick-up the car.
From my experience, any Homelink devices that you may have programed (like garage doors) will not get carried over and you will need to reprogram the homelink unit.
Note that there is a slight difference in the reset functionality for the screens. Currently your car with AP1 has two different resets ... pressing the scroll wheels resets the main center display. To reset the instrument panel you need to do a separate reset using the two buttons above the scroll wheels. After the MCU2 upfit there will be just a single scroll wheel reset and this will reset both screens at the same time. Reason for this is that the instrument panel is now just a slave display off the the main MCU processor, and not it's own independent processor as with MCU1.
One tip ... make sure before you leave the service center than you can not only connect to your car with the app, but lock/unlock/start climate control via the app. Some have had problems where the service center forgets a step to fully enable app capability, or for some reason it doesn't take the first time.
Hope you continue to enjoy your (new to you) car.