When I moved to the Mac, I was happy to find that most of the preferences were put in one place. That makes things a lot easier to find. Mac’s convention of having all preferences in one, known place is inspired.
New in version 3.1, if I’m not mistaken, are two new preferences that aren’t where I’d expect them to be. IOW, Appearance and Theme have their own menu item. Looking around at a bunch of apps, there are none that I’ve found that do that.
“Theme” in the “Scrivener” menu is a quick way of accessing exactly the same feature via the “Manage…” button of Preferences. “Appearance” does not belong in the Preferences. Other apps that have the ability to switch between dark and light mode often put this in the “View” menu, but that is entirely the wrong place for it since it does not affect any particular view but the entire application; it is thus in the application menu, where it belongs.
Both of these are things users are likely want to switch frequently. The whole point of a theme is to allow users to switch between different sets of preferences quickly. Preferences - as in the Preferences panel - are things that users are likely to want to set up once and then leave.
The “Theme” and “Appearance” menus are literally two of the coolest new aspects of 3.1, and most users so far seem to appreciate them.
I can see why you would prefer to have everything bundled in preferences, but for me having fewer clicks for this special task seems to be more comfortable than having to look through the preferences submenus to find those commands. Same goes for the View menu, which though would make it more comfortable than having them in preferences again in my opinion. But yes, initially one would expect them in preferences.