How to make Certbot respect Debian standards for certificate deployment?
If I were to do this I would leave the /etc/letsencrypt tree exactly as it is (because anyone seeing the use of LE would expect it) and then use my configuration management tooling to create symlinks in the /etc/ssl tree as appropriate to point to the symlinks in /etc/letsencrypt/live/CERTNAME directory.
The documenation does mention changing file locations too but I don't know if it will be possible to do what you want.