Is this just a Debian (and derivatives) feature, or more common? I just spent nearly an hour trying to figure out why the link file changes I'd made on a system were not working properly, and this was the cause. I even ran 'networkctl status' on an interface that should no longer exist, and it reported a 'Link File' path that did not exist... because it *used* to exist (in /etc, not /usr), and had been copied into the initramfs.
At a minimum, I'd like to suggest to the relevant distros that they modify systemd.link(5) to clearly indicate that this behavior exists and that any changes to link files must be accompanied by an initramfs update or the behavior on the next system boot may result in a non-functional network.
