The documentation still mentions a way to use commercial certs: https://docs.aegirproject.org/usage/advanced/ssl/#commercial-certificates
I too have run into the problem aegir_https not working the same way regarding chain certs.
Running aegir3-provision/stable,stable,now 3.182
LE is not an option for our org unfortunately.
Is there a way to use commercial apache certs with aegir_https/hosting_https?