Done, update released. The field is Website > ... > Advanced > Custom top-level configuration. Its content gets inserted before the website's server{} block.

Fixed

I hereby allow you to install phpMyAdmin manually.

No, but you'll be able to give permissions to yourself as long as you have access to the Configure plugin.

Installing to /usr/share is a bit of unfortunate idea, so I've put together a small tutorial: http://support.ajenti.org/topic/479448-/

Done in df15207 (will be 1.2.22.1)

Create a separate user and give him permission to access Configure section and to modify configuration, and continue from there.

No, but you can forbid login by setting an empty password. Be sure not to lock yourself out of the panel though.

Sorry, but we don't have any built-in backup capabilities. You might want to try CrashPlan or another automatic cloud backup solution.

It's currently not possible. What is the exact use case of having multiple FTP accounts for one website?