I was maybe not clear enough and should have added that all my VM run already a fresh Atomic Fedora delivered by the hosting company.
So my idea is to "share" what I added in one machine (/etc settings and layered packages, let's call the machine "origin") to other machines (targeted VM) in an automatic way.
It seems that articles about automate building atomic host[0] will indeed do the trick. In this way, I will just need to install/configure origin and build the other according to. Same for any future changes.
The only thing I was thinking of adding is to put in the "middle" a github repo to store the machine state. This would be the path: machine origin ---> github repo "My OSTree" --> targeted VM. But maybe it is not possible and best is machine origin --> targeted VM.
Am I in the right path for what I want to do?