Specifically it's Pocket Edition 0.15.4 which was released July 2016. The devs have said they plan on continuing to work on it for 6-8 months minimum to add more features including 3D, multiplayer, and later version features. For the sake of developing an initial version on the very limited 3DS hardware, they had to branch from the most recent version at the time they started work on it and get that fully up and running before moving forward.
For example in the stream they said after bug fixes on the current version they plan on getting into 0.16 next which added ocean monuments, prismarine etc.
When they say "no Better Together" they mean day-and-date with the other versions, it very well could eventually reach that feature set.