Join Bobby Owsinski for an in-depth discussion in this video Exploring the Mastered for iTunes format, part of Mastering for iTunes.
Master for iTunes is a program that Apple introduced in 2012 where the iTunes store accepts high-resolution master files and provides higher-quality AAC encodes as a result. Music files that are supplied at 96 kHz, 24-bit, will have a Master for iTunes icon placed beside them to identify them as such, although any sample rate that's 24-bit file will be considered. Master for iTunes does not mean that a mixer, producer, or mastering facility does anything special to the master except to check for what it'll sound like before it's submitted to iTunes and then check it later again before it's posted in the iTunes store.
All encoding for iTunes will be done by Apple, not by the mastering house, record label, or artist. The reason for this is to keep the encodes consistent and to prevent anyone from gaming the system by hacking the encoder. This also avoids any potential legal problems that might occur when a mixer, producer, or mastering house sends the files directly to iTunes without the label's permission or uses different submission specs. Master for iTunes is only an indication that a high-res master was applied, it's not a separate product. There will always be only one version of the song on iTunes, and it will be available at the same price regardless of whether it's mastered for iTunes or not.
Master for iTunes doesn't mean that the song will cost more in the iTunes store or doesn't mean the iTunes will charge for you for the service. Everything is like it was before, you just apply a high-res master so it ultimately sounds better to the listener.