It looks like the bug is still present in some form, as since I updated to BigSur I am unable to open message:// URLs using the open command. This is explained in details in this StackOverflow question - https://stackoverflow.com/questions/66269941/bigsur-open-command-does-not-handle-message-urls-anymore-workarounds, but in brief, the following command would have worked in Catalina (by opening a specific email in Mail.app)
open -a "Mail.app" "message://CALoR5A+vANPG9eCcHRHnO@mail.gmail.com"
while in BigSur it leads to the following error:
The file /Users/macbook/message:/CALoR5A+vANPG9eCcHRHnO@mail.gmail.com does not exist.