It's open middleware, just like the glibc resolver. For example, it's entirely possible to force applications to use the glibc resolver, just dont let them open sockets to anything but 127.0.0.1:53. They wouldnt be able to use http/https either in that case, but that's the point.
If you are thinking about side-channels like HTTP over DNS(S), then fine, but the middleware can see the traffic because that's it's job. If the app starts making encrypted requests atleast you would know, and since it's open source the user can fix it and tell everyone the application is using a side-channel to subvert the user.
_But that missed the point._ The app wouldnt have DNS code in it. It would only be able to ask to map a name to a record. And even then, that misses the point too. In the end it wants to fetch a URL, and what I am talking about does that. Firefox parses a GET it was handed, and if it wants to make additional GET/POST's, then hand them over. No DNS or networking code needed in the browser. Linking to a SSL lib would be a bug.
Reaching into an arb open source app and getting ahold of it's SSL machinery to MITM it is always a moving target (aka deliberate problem), and that's an anti-user feature.
Common middleware that handels the comms (SSL etc) (os or application level) levels the playing field. The recent DoH changes would have been up to the user, because that code isnt in the browser any more. Users are leveraged by the browser vendors, "want the latest version?" "hey I see you are using a 0-day browser?" and forced to swallow or fork. I realize users can disable DoH, but again, that's the point. It's a moving target. They can just keep "fixing" the defaults.
Same thing with Chrome's recent changes regarding the DOM blocking API. If Chrome was forced to deal with asing for URL's instead of fetching them directly, it wouldnt matter. The blockers would operate in the middleware.
As I mentioned in my original comment, the point is to axe the networking code from the applications, and force them to make requests a layer up. This is not like forcing them thorugh a SOCKS proxy. It's deduplicating the code, and making the parts seperable. The monolithic nature of browsers isn't some accident.