Unfortunately, there’s not a good way to use Certbot on Amazon Linux. certbot-auto has never worked well on the platform (see this post for more info) and we haven’t been able to get Amazon to package the project.
If unsetting PYTHON_INSTALL_LAYOUT doesn’t work for you, I think your best bet is to use a different ACME client but I am unfortunately not familiar enough with any other than Certbot to give you detailed instructions on how to use it.