That said, I also think that there’s no absolute truth for what constitutes a “specialized use case”. I think if I’m the operator of a network, or a computer, or a container, or an application, having it use custom DNS settings is up to me. And Firefox/Chrome enable that: the operator can change the setting to whatever they want.
Speaking to the default case, Firefox/Chrome moving towards DNS defined at the app layer smells painful to me as a network operator, but ISP DNS interception also smells to me, and for the normal consumer threat model and network topology, Firefox/Chrome using CloudFlare DNS is essentially pure win. Most consumer users aren’t on networks with split-horizon DNS, and most consumer users aren’t at risk from CloudFlare logging their DNS requests, even assuming they’re violating their published privacy policies.