Yeah maybe, who knows. I use privacy enabled DNS-over-TLS service (stubby) running on the loopback interface (127.0.0.1). The first time this happened I didn't even notice for a few days during which I had no DNS privacy thanks to the macOS upgrade, hence automating the check...
If like many people you use the default DHCP supplied DNS service from your local router you wouldn't even notice this problem since it's the default and apparantly Apple preferred option.
Here you are running into conflict between Apple philosophy of "we will make it work for you" and your philosophy "I want something special". I think that users like you - running highly customized setup - would really be happier with some version of Linux. May be on Apple hardware, may be something cheaper from Windows side.
MacOS upgrades seem to reset special configurations when they are installing new upgrades for that system area. Network is critical component today and, for 99.9% of people, default settings are working fine. Well, mostly they are working fine, there are exceptions...
Apple chooses to impose its "walled garden" approach and resets customizations so new configuration they push in works. Makes sense and if I was doing it, I would do the same thing. It must work after upgrade or people will be screaming that "Apple upgrade broke it".
This is saying nothing negative about your needs and configurations - and nothing negative about Apple approach. But keep in mind, that you are not the real target Apple customer, you are outlier and, to be fair, they do not care about you too much. They care about those thousands of non-expert users, whose apple devices "just work" (well, mostly...), like my daughter. Her computer maintenance is go to Genius bar and hand them the computer with "ain't working right". Those are their real customers.
Your choice is live with Apple walled garden somehow or change system. Again, nothing wrong on either side of that - it is as it is.
For me, I impose all of these network security things on highly customizable wifi router. It is the right place for such configuration changes. And I do not tinker with my macOS and iOS settings, they work just fine for years. This way they
also work inside my workplace (with aggressive IT). And if needed, I run vpn through home when outside.