How to deal with permissions on Linux, run wp-cli and have Lets Encrypt installed?

Hi, I am mostly a WordPress developer and investigating Docker for easy local setup.
So far, I have managed to have what I want, and generally, it works: WordPress, phpMyadmin,…
I have a separate network container and hold some configuration files outside so I can use them everywhere (this is now just testing) - just to say.

There are some quirks and a few things I would like to add:
1)
Permissions - using Linux, when the container starts it is under root/root, and the only way (so far) to edit the files is to change the ownership.
By doing that, WordPress cannot install the plugins for example.
Is there a way to go around that and have both?
I know I can do that manually, of course, but sometimes it just needs to work.

Is there a way to run wp-cli on boot?
I would like to run the command to install WordPress, etc, (when I am starting completely new, when I have files and the database current setup is fine.)

How can I add Lets Encrypt SSL to avoid later database search and stuff? :slightly_smiling_face:

My docker-compose.yml: https://pastebin.com/embed/guNHP3sN

Thank you in advance, any advice is highly appreciated!