The short answer is no, I was not present at all when the Ex was being worked on, in fact since I had to be at work, I simply dropped the car off Wednesday night at the dealership with the note that MFT was stuck in a reboot loop and I tried fuse 29 and battery cable pull without success.
Got a call Thursday afternoon that they couldnt do the software update and that it needed a new APIM, which were already on order (obviously a sign of more wisespread issues) for delivery tomorrow. They called me on Friday saying it was replaced and ready to go.
Some settings were reset, such as the clock, however other settings, such as Sirius presets were still intact. To reiterate, I was never having anywhere near the number of problems as Loganfilm, before this reboot loop. I would have been happy with just a software update to "unstick it". I never mentioned APIM replacement to the dealer, they brought it up on their own. So they would have no reason to tell me a new APIM was being installed, when I would be just as happy to get the Ex back to the way it worked for 2 months even if it only required an update from 2.7 to 2.8.
I did think it's odd that not all my settings were lost, but I'm also not sure if the APIM is what houses all the memory for MFT.
In the end, I'm happy to be back to where I was, because, while not perfect, MFT was performing "ok".