I was looking into this again today. As I mentioned in the pull request, there is an issue with the draft PR. What happens is that the current config is retrieved using the command show configuration commands instead of show configuration. The output does not contain any less specific config paths, as they would be useless in configuring a system. However, when determining what to delete, this information is essential.

I was looking for this too, and actually started to play with the code of the module to get this feature in a few weeks ago. I've submitted my changes as a draft PR on Github. I've been playing with managing my VyOS config from SCM for my home lab. It's important when I for example remove a firewall rule, it is also deleted in the running config, instead of being orphaned. It seems to work pretty well in my setup, but I am uncertain if nothing breaks in other workflows.