"Git version control for WATO" - what about versioning other facilities like web settings and reports?

I strongly recommend not to do that! You might break Checkmk in some unforseeable way, if there is an unexpected folder (read symlink) there. Probably nothing will break immediately, but ultimately you might get hit by that.

First I want to stress that that setting only creates a local git repository. You might want to create a cronjob, which pushes this changes to a remote server like a GitLab instance.

Second I think your idea won’t make it into the product, as there is little demand and it can be overwhelming to some people. On the other hand I see no problem in you creating your own commit cronjobs, that just run say hourly and commit all changes in the directories you deem interesting.