I looked into this to see what it takes to change this and it doesn’t seem too involved, but I don’t think the preferences are the right place for this setting. I agree that this being per editor is really bad but making it per scene (just like the snap setting) seems reasonable.
Similar to what you described, I find the auto-offset useful when plopping down a lot of nodes quickly in the beginning and later disable it once I’m organizing the tree. Based on that it makes sense to me to be able to toggle this during a session without having to dive into the preferences.
Disabling auto-offset in your start-up file would then still mean you’d never encounter it unless you explicitly enabled it. Do you think that’s an acceptable compromise?
I also wanted to plug this feedback thread for changes to how joining into frames during transform works:
I had hoped to get a few people to test this to get some feedback on the direction and to make the behaviour solid before bringing it up with the core team. 