Custom key bindings can be used to introduce simple keyboard shortcuts for your most frequent actions. For example, you can bind keys to jump to specific mailboxes or toggle IMAP keywords. MailMate is distributed with an example keybindings file which shows how to create most of the key bindings available when using Gmails web interface (if you have key bindings enabled in Gmail). Other webmail clients have different key bindings. One example is fastmail. If you create a key bindings file for your webmail client then I encourage you to share it by letting us include it in a future update of MailMate.
The chapter about hidden preferences is a collection of all the features which can currently only be enabled using the Terminal. Previously these preferences were only described in the release notes. There are simple preferences such as for enabling alternating row colors and there are preferences for advanced experimental features such as rudimentary support for OpenPGP. I encourage you to look through the list yourself.