So here is the issue. MyFord Touch does not appear to use the "iPod Out" feature of iPhones/iPods. This taps into the iPod database and just presents you the data. This is a good thing though as that feature (iPod Out) is not supported by the new "lightning" dock port. Thankfully it appears that MFT actually scans the device and finds all the music & playlist files then presents them to you in a very similar way an iPod would. So when you have iTunes Match enabled there are no files on your phone, at least in the beginning. As soon as you play a song once it downloads it to the device. The next time you connect the phone to MFT it will find those files.
So it is actually a good thing that MFT handles iPods & iPhones this way. If it didn't the new iPhone probably wouldn't work with MFT.