I think this is rather orthogonal. A non-well-behaved app can use hardcoded DNS servers as well. And if the author is concerned with your ability to intercept and filter it on protocol level, they can always hack their own equivalent of DNS-over-HTTP with a basic REST service.

OTOH I expect non-malicious code to just use the platform/language/framework-standard mechanism to resolve hostnames, and I expect such mechanisms to provide all the necessary customization points, just as they did for DNS.