hi @SilentImp
Are you open to use other clients?
There are a couple of good Bash Clients (GetSSL and ACME.sh) which do not have python dependencies and have a high level of automation
https://letsencrypt.org/docs/client-options/
The reason why I mention this is that by the looks of it your servers python configs need a bit of work and there is a benefit vs reward analysis which can be done here
If you want to carry on fixing python in the virtual environment then that’s ok as well.
I believe your issue is that you do not have the intermediate required for downloading packages over SSL from PYPI.
Have a look at this article on how I built certbot on windows: Running Certbot on Windows - Phase 1
A lot of the steps are not relevant to your setup as you are on linux but there is a note about missing intermediate certificate
Andrei