I recently tried to enable system-wide DNS over https on Fedora. To do so I had to to some research and found out how comfusing it is for the average user (and even experienced users) to change the settings. In fact there are multiple backends messing with system DNS at the same time.
Most major Linux distributions use systemd-resolved for DNS but there is no utility for changing its configuration.
The average user would still try to change DNS settings by editing /etc/relov.conf (which is overwritten and will not survive reboots) or changing settings in Network Manager.
Based on documentation of systemd-resolved, the standard way of adding custom DNS servers is putting so-called ‘drop-in’ files in /etc/systemd/resolved.conf.d directory, especially when you want to use DNS-over-TLS or DNS-over-https.
Modern browsers use their buit-in DNS settings which adds to the confusion.
I think this is one area that Linux needs more work and more standardization.
How do you think it should be fixed?
Could also look at tailscale, set it up on you home PCs and mobile devices, set the magic DNS to a home server or vps running pihole. If you don’t like the aspect of tailscale being controlled by a third party you could self host that part using headscale on docker as well