For NetworkManager it'll write the config file to /run/NetworkManager/system-connections/ and for networkd to /run/systemd/network/ on EVERY boot since /run/ is a tmpfs (file-system in RAM).
For almost all servers, and most workstations, netplan is an unnecessary indirection since most hosts (including containers) have pretty static network configurations that only require writing once (to /etc/NetworkManager/system-connections/ or /etc/systemd/network/ ).
nmcli is the NetworkManager command-line tool. There is also nmtui for a text user interface. These are terminal alternatives to the GUI applets such as nm-applet (network-manager-gnome) or plasma-nm for KDE.
networkctl is the CLI interface to systemd-networkd. There is no widely used GUI interface to it (yet).
Linux networking and DNS resolution, while working fine for the happy path, are a dumpster fire from a system management viewpoint. Especially if you want to do anything even mildly off-script. And I say this as a Linux user since before the kernel hit 1.0.
I don't know, maybe it's just a documentation problem. The accumulated junk of 50 years of obsolete documentation that you have to wade through to find out that the whiz-bang Linux distro you're using today is not the Linux which worked fine last year.
The exit off my lawn is in this direction.