@Mind-Brain:
Last week I have performed the test you suggest.
I have tried to copy the .ini from one project to another and altering it (from ProjectB to ProjectA).
Then ProjectA behaves almost as expected:
When opening ProjectA the unreal source control is enabled and history works fine.
But if from the Unreal Editor I modify the source control configuration and quit Unreal, then the ProjectA .ini is not modified on disk!!! So the just-made modification is lost.
We are still trying to isolate the root cause of the problem. Any additional idea is welcome.