v9 will not support Hyper-V 2016 for sure.
When we do release support for Hyper-V 2016 (which will happen 2-3 months after it goes RTM), we will probably support both options for changed block tracking, as our own driver will likely be a more reliable choice until Microsoft's own changed block tracking technology matures. However, there are no firm plans yet, and our current intentions may change.
That said, we will definitely support MS RCT API in our very first release featuring Hyper-V 2016 support.
Yes, MS RCT API does support 3rd party SMB3 storage.