Hello there,
This has taken us aback. Here is some info: Replit Create a .env File Changed
Otherwise, Replit still natively allow access to environment variables using process.env, but this has to be done through a Node (or other) server - not the Shell terminal.
As you say, you can no longer comment out variables, but you are able to just change the name (key) to anything else (add a letter), and this should achieve the same.
Hope this helps