A bit confusing I agree. Just a little bit research.
Linux
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Linux is a family of open source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991 by Linus Torvalds. Linux is typically packaged in a Linux distribution (or distro for short).
Distributions include the Linux kernel and supporting system software and libraries, many of which are provided by the GNU Project. Many Linux distributions use the word "Linux" in their name, but the Free Software Foundation uses the name GNU/Linux to emphasize the importance of GNU software, causing some controversy.
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I wouldn’t call it a mess. There’s a reason it’s not standard. It’s because Linux is about having choices. Linux users have such a variety of use cases and there are a zillion different kinds of hardware it runs on. There’s no one thing that works for everyone.
I think this flexibility is a big part of what makes Linux special but also what makes it difficult for newcomers. The documentation on all the various software is typically very good to excellent. The harder part is figuring out which choice to make in the first place.
I don’t really have any answers except to take it all in and be more willing to do some research than some other platforms may require.
System-wide DoH is sort of a power user thing to begin with so other platforms will likely be similar. I think you would probably be using some kind of app to do it on Windows or Mac.
By the way, you might want to take a look at stubby for your situation. I did something similar a few weeks back and that’s what I used. It’s runs a little local DNS proxy that forwards requests to your upstream servers. Then you would set your DNS server to 127.0.0.1 in NetworkManager or whatever you’re using. You have to change like 3 lines in the default stubby config a typical distro may provide to make it work.
Well, I'm not using systemd and Portmaster (safing.io free open source without the VPN tunnels) has a DNS control over any request your Linux do... I don't think I have any issues here... hehe
Its bad if you dont like having a bunch of options for your network stack.