To my knowledge, there are not different versions on MoviesAnywhere. So a store (MSFT in this case) could have no extras on a title but MA will have them and vice versa. You can see this if you search on a title in MA, that only one shows up whereas
MSFT could have multiple "bonus" and "non bonus" versions.
In the cases of the LOTR Extended and Big Hero 6 noted, I see extras (and only one version) on MA for those titles. As the person who originally posted this (Thorlakur) deleted his post that JasonoftheD34D replied to, I assume he found that some of the
extras were actually there in MA and he wasn't seeing them in whatever UI he was using at the moment.
To JasonoftheD34D's comment: "If you're able to switch from the bonus content versions to the non-bonus that'd be great.", I assume you are referring specifically to MSFT Movies, nothing to do with MA. Why would you want this? Only thing I can think
of has to do with some of the older "bonus" titles where they have the extras tacked on to the end which is an f-ing terrible experience. They don't do this with new titles I don't believe, but haven't gone back and changed older ones.