I took it to the dealer today and they brought it back out saying I had to remove the aftermarket tune I had in it. I don't have any tuning on my car. They thought I had a COBB AccessPort, because my phone holder looks similar to the holder for that. I also have dual ScanGauges plugged into the OBDII port. Those I transferred from my 2011 SES. It turns out that having the ScanGauges plugged in was somehow affecting MFT's ability to collect the data it needs for the Vehicle Health Report. Once we disconnected the ScanGauges, it no longer complained about having less than 200 miles on the odometer. It then said it couldn't collect the data and to try later. I drove it home (~15 miles) and then tried running the report again and it worked. I'm not sure if it's specific to dual ScanGauges, or if one of them being an older model is causing the issue. I wonder if having an AccessPort plugged into the OBDII port will prevent the VHR from running?
I never considered the ScanGauges as the source because my 2011 SES was able to run the VHR with those plugged in. I guess the way MFT runs the report is different from the older Sync system.