Thanks for reporting Aaron, that sounds like a bug...

I'm a bit bogged down with some high priority stuff but I'll swing round to having a look at that ASAP.

In the meantime, our WordPress appliance ships with 'wp' aka WordPress CLI preinstalled. We also provide a helper/wrapper script named 'turnkey-wp' which runs as 'www-data' so the filesystem permissions don't get messed up. Other than explicitly running as the webserver user ('www-data') in the WordPress webroot (/var/www/wordpress) it should work exactly the same as the default 'wp' - except better. If you hit any issues, please report them.

As to setting/updating the admin email, 'turnkey-wp' should be able to handle that no worries. I haven't tested myself but a quick scan of the docs suggests that this should do the trick:

turnkey-wp user update admin --user_email=NEW@EMAIL.COM

As noted above, using 'turnkey-wp' - instead of vanilla 'wp' - should "just work" but please let us know if you hit any issues. If you do hit an issue, to avoid having to wait for a response/fix and/or to confirm if it's an issue with our wrapper you can just use 'wp' directly. IIRC you will need to change dir to the webroot first and then fix permissions after. I.e.:

cd /var/www/wordpress
wp WHATEVER COMMANDS
chown -R www-data:www-data /var/www/wordpress

Also here's a few links that might be handy and save you a google is my command isn't quite right and/or you want to do other stuff with it; general 'wp' commands, 'wp user' commands & the 'wp user update' command specifically:

https://developer.wordpress.org/cli/commands/
https://developer.wordpress.org/cli/commands/user/
https://developer.wordpress.org/cli/commands/user/update/

Hopefully that gets you going.