I don't believe VFS for Git will ever be abandoned by Microsoft, but I'm doubtful it will ever get any more major improvements from them.
Scalar does use the VFS for Git client-server protocol, and both Scalar and VFS for Git rely on the same improvements to the git app itself, so I could imagine that GitHub would adopt the GVFS protocol and support Scalar without formally supporting GVFS itself.
[1] GitHub did announce future GVFS support in 2017 - https://venturebeat.com/2017/11/15/github-adopts-microsofts-... - but if anything came out of that I don't see it in GitHub help today.
Scalar also supports Windows and macOS, while VFS only supports Windows: https://github.com/microsoft/VFSForGit/blob/v1.0.21014.1/doc...
When I left Microsoft about half a year ago, GVFS and Scalar were both in heavy use there.
Right now we don't plan on supporting it; most of our work is focused on upstreamable changes and opinionated defaults. But that could change if we're missing some important use cases.
Feel free to email me - my HN alias @github.com - if you prefer to discuss privately.