Sorry, I missed your question in this thread. I think I understand your question, but I am not sure.
The answer is that I discarded this way of applying initial settings. Activating the 3D39 client modifies the Orbiter_ng.cfg file. So there is a tie with all the other checkboxes of activated modules. That's a bit unfortunate.
I changed these scripts a lot since then. I ended up with a folder which contains all files which I consider 'Orbiter core files'. That includes the D3D9 client and any personal changes. These files will be included in the first snapshot.
Working this way means you can't use an add-on manager to activate and de-activate different graphical clients.
If you find a better solution, please let me know! :thumbup: