You're right, they're somewhat hardcoded. :-) The reason for this is that eZp didn't really have a menu system before. The navigation part solution is also kind of a hack. Right now it is a bit messy, but it works. We'll probably improve this part of the system sometime in the future; maybe during the 3.7 cycle. What kind of extra menu do you wish to create? Just some shortcuts to existing functionality or do you wish to implement your very own submenu for a custom/home-made module?
I need to implement my own submenu for a custom module. If this isn't possible without modifying the template code of the admin pagelayout, then what's the point of having INI settings for the dynamic inclusion of top menu items in the first place?