My 2016 MX had the eMMC replaced, and then another time had a full MCU replaced. (Fortunately both times fully covered under warranty.)
Some tips to consider after the MCU replacement: yes, they should do a save and restore of your profile information, but you'll probably have to reprogram your garage door opener and your bluetooth pairings. You might have to reset your seat configurations. And whatever saved trip mileage counters you had will probably get erased. You should also look closely at your dashboard and make sure everything was reassembled properly, with no extra gaps or other loose fittings in and around the main screen and vents.
But in the grand scheme of things, it is pretty easy job and (other than the points I mentioned) you shouldn't notice any differences.