@Zaq,
Sent you a node.cfg file which has been upgrade many times with patches. You can see the file has gotten bigger and has dupes. What might work is the approach of reading in all the keys and then generating a fresh/clean file which does not try and merge into an existing file. As long as there is always a backup, that approach seems like it would keep the file clean.
The above list is a good amount of work for me on each upgrade. We don’t want clients to have printer or SMB support and we only allow them to use GNOME. These types of things would be the reason I would never enable automatic updates. It seems great to reload the keys with paths and features, but the actual concept of enabling them seems like not the right approach on an upgrade. I do understand that you are trying to find the balance between plug-and-play and power users that have made customizations.