If this helps, the specific platform my hosting provider requires that the common name be set to the domain name with the "www" in front, due to this platform being created before common name was deprecated. I've alerted their engineers to this impending change. The CSR workaround is allowing me to install the certs again, though it's causing a lot of manual labor for me as this specific platform requires CSRs to be generated through a web UI. Yes, I am looking at moving hosting platforms, but I've got around 1800 websites with certificates to migrate, so it's not a small project.
I had come to rely on this behavior since there is advice from community leaders in this forum (albeit, several years old) saying that the common name is set to the first domain name specified here, and the official docs didn't really say anything that I could find. Here's the comment: How can I easily make the Base Name and Common Name the same? - #2 by Patches
Is there any general sense of when Let's Encrypt intends to remove Common Name altogether as mentioned here by @jsha : Domain ordering not respected, unexpected certificate subject - #6 by jsha ? Weeks, months, years?
The entire removal of the Common Name is the worst-case scenario here for me since my hosting provider would stop accepting all Let's Encrypt certificates if they aren't able to make the change before then or if I can't migrate away in time.
Since there is a Common Name being chosen by Let's Encrypt now, a new command line parameter to choose the Common Name seems like it would have very little downside, especially if it issued a deprecation warning. This would still allow issues to be raised in situations like mine that require updates to follow the new standards while allowing for a longer time frame for this migration. It may not an easy or quick change for everyone (it's not for me).
Thank you for your consideration.