Right—part of Apple's job is to create an environment where the "correct path" is clear and developers want to follow it. Either Apple used to do a better job, or else developers did.
And, consider:
• Apple encourages developers to distribute via the Mac App Store as much as possible.
• Preference Panes cannot be sold in the Mac App Store.
• In Catalina, all Safari extensions must be installed from the App Store as individual apps.
• New Notification Center widgets are always installed as applications. Old Dashboard widgets never were.
I would say that taken together, the clear implication from Apple is that apps are the way to go. And it all comes back to the Mac App Store, which Apple wants to push that at all costs. Evidently, they either actively don't want to sell non-apps in the store, or they don't care enough to build that functionality.
There are probably times when Apple's patterns are just wrong and the community coalesces on something better—I can't think of any, but it has probably happened, or will some day. But I do not think this is one of those times, because if you step back, using an app does not make objective sense.
(P.S. It's interesting to note that Apple's own iOS apps tend to have far fewer in-app preferences, in favor of sticking stuff in the Settings app.)
