I do not see any problem with this, I think its a wanted feature not a problem.

when I remove the machine I expect all its files are removed. it is the administrator who decided to remove the container at the end, so this is consistent:

Persistent settings files created and maintained by the administrator (and thus trusted) should be placed in /etc/systemd/nspawn/

because it is the administrator who decided to remove the machine, and a machine means both: the image and its config files

I do not not want to remove a machine which leaves its related config files, this will force me to do more cleaning!