No, there are tons of apps that can interact with cPanel through cPanel. Those are cPAddons or Plugins - they operate entirely within cPanel.
The next thing is the cPanel hook interface - this relies on normal cPanel actions like when a cPanel user account is created - or when a bill is sent through the WHM. There isn't a hook for to initiate a process, like adding e-mail accounts... There are hooks for automated processes.
But like you said, cPanel is just the maintenance app. All it does is control other things. So you could, in theory, interact directly with the mail server app. In which case you wouldn't want to talk to cPanel at all.
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