I ran some tests and was able to conclude the following:
The Entune system is definitely using the FAT information to determine play order rather than the ID3 tag information. If you sort the files' order in the FAT alphabetically by their filename by using an app such as DriveSort (http://www.anerty.net/software/file/DriveSort/
) or FAT Sorter (https://fat-sorter.software.informer.com/
) before the USB drive has been plugged into your car with those files on it, then those files will be displayed and played in alphabetical order by Entune. If you don't use an app to sort the files order in the FAT alphabetically by their filename, then they will likely be displayed and played in the wrong order by Entune because the files' order in the FAT often doesn't correspond to their alphabetical order.
What's really frustrating is that if I plug a USB drive in with a folder of files whose order in the FAT has not been sorted alphabetically by their filename, then remove the USB drive and sort the files using one of the apps listed above, when I plug the drive back into the car the files will still
be in the wrong order even though I can verify on my computer that the files' order in the FAT corresponds to their alphabetical order. It's as though Entune is storing the first file order it reads and not updating it when it changes. Throughout all of my testing I did experience a couple of instances in which a folder whose ordering of files in the FAT was updated to alphabetical order after the drive had already been read by the car suddenly had its files displayed in the correct order by Entune, but I was not able to determine what the trigger was for this.
In short it seems the only way to have files within a folder play in the proper order is to copy them to the USB drive and then run a program such as DriveSort or FAT Sorter, all before
plugging the USB drive into your car and giving Entune a chance to "see" the files in the wrong order. This seems like a huge hassle given that the 10 year old stereo in my previous car was able to key off of leading digits in file/folder names and automatically play in order based on that. Given that I only listen to podcasts and audiobooks now, the ability of a car stereo to play files in a specified order is key.