No you don't need to copy them out of that folder. You just need to edit the file and put your website name where it is in the template.
Ex. plex.thisismyrandomexamplewebpage.edu
Make sure you enable viewing file extensions cause the templates are all inactive by default.
To activate the file rename it from subdomain.radarr.config.sample to subdomain.radarr.config
If you install the letsencrypt docker from linuxserver then it should come with template config files for radarr sonarr and plex.
It should be in the proxy conf folder in the appdata folder for letsencrypt
I can upload a template for you later if you need it.
Just wanted to add that in order to get webhooks running the plex docker has to be in HOST mode. I had mine on bridge mode since I was using it with the letsencrypt docker. (there is a way to use letsencrypt in host mode I just had no reason to before and was lazy).