nbdev works with any kernel, because it only cares about the notebook files, which as you know are just JSON.
I've been using it with xeus-python kernel lately.
Edit: Forgot the Git part. It was designed to handle the git limitations in notebooks as well. In fact, one of the commands in the tutorials is to set up it's built-in git hooks, which will run special clean commands on commits.
My main issue with notebooks is putting them under version control in git. This seems like it could help with that.