Why does this happen in the standard error when I run certonly or renew?
Non-standard path(s), might not work with crontab installed by your operating system package manager
That's a question for the certbot devs: certbot/certbot/src/certbot/_internal/client.py at be5a9966ac2a737243ddfc6198817a6331de543a · certbot/certbot · GitHub
It triggers when your certbot config/work paths are different from the defaults, so they are presumably telling you that permissions etc may or may not need some work:
I think that happens when you have specified the --config-dir option to override the default config location. When you do that you must use that same --config-dir value for every command for that config. That includes the renew, certificates, reconfigure and redoing the original command you used it with.
Depending on how you installed Certbot there was a cronjob or systemd timer setup to run the renew command. If so, those rely on the default path and does not know any custom path you used with --config-dir.
Personally, I think --config-dir creates more trouble than it is worth. If you need complex control of the directories in a large install I think other ACME Client solutions are probably better.