Comment by dwaite
I would feel far more concerned that an arbitrary application that decided to do its own DNS resolution would be doing so for nefarious reasons, or might mess up the process (such as not supporting encrypted DNS in this case).
If you genuinely cannot trust the OS vendor, you don't try to tinker around in user space but you stay off their platform. Personally, this is why I don't have any machines with a Microsoft OS, and why I don't have a Playstation.
The concern isn't that Apple controls the OS and so could do nefarious rootkit type stuff, but rather they may try to nanny through the framework they prefer and push for all apps for their platform to be developed in.