The kresd executable doesn't consume YAML.  You need the new knot-resolver executable (written in Python), which is presumably missing in your case, along with kresctl.

I can add that consequently also the init scripts need to be reworked, etc.

Because instead of you/init starting individual processes (kres-cache-gc and multiple kresd), you only start a single process like for most daemons and the herding happens automatically based on your configuration and essentially the same way on all platforms (Docker, FreeBSD, systemd).

Here's a nice picture of internal architecture:
https://www.knot-resolver.cz/documentation/v6.0.17/dev/architecture.html