“Modified Site Container” in this case means going into the container and running commands to install packages (apt), change around core files, etc. We show this warning by default since it’s tough to know if changes have been made to a site’s container that’s running the Custom environment.
You’ll be good to go if all you did is switched around the web server and/or PHP/MySQL versions! Also, the conf directory will be backed up prior to upgrading/switching Environments.