We are having problems with the web authorisation process because we have multiple web server behind a load balancer.
What would be ideal would be a local authorisation file to be written to disk and the script to pause to allow an advanced used to copy the authorisation file across the cluster. After this the keys and certs would be written locally in an output direct for manual installation by and advanced user.
For us this would allow us to drop the certificates into our AWS ELB autonomously via the Amazon API with an IAM Role.
This would solve a lot of your advanced user issue around authorisation of domains and configuration of clusters,