Apps like Total Commander or Nexus Media Importer don't exactly mount the flash drive. You can access files off the flash drive, but as far as I know you can only access the files through the app. You're at the mercy of the app to let you open individual files in another app (e.g., through Total Commander you can open a movie file with DicePlayer).
But since the flash drive isn't really mounted in the normal file system, other apps can just go in and see all the files. This means media cataloging apps (e.g., Mizuu) and music players don't really work well.
This is a disappointing change. I'm not going to root my Droid Maxx over it, but I did root my Nexus 7 tablet largely to get around this limitation.