@zensaiyuki That GNOME case does show something interesting: It may be useful to have behind-the-scenes options to allow different platforms to share code, whilst not exposing it to end-users because it might/will break stuff. Also makes it easier for *some* apps to target a selection of those platforms.
But in terms of UX this essentially comes out to the same thing as you're saying.
@zensaiyuki In the case of browsers, the question seems to have always been not whether to have configuration but who should be configuring these settings.
The standards now say that webdevs have ultimate say whilst browsers provide defaults. The problem though is that the defaults are no longer reasonable, and webdev's final say can't always be trusted for reasons you've described in other toots.
Fairly trivial to fix when I'm not worrying about breaking JS...