When a mod needs to add new menu items to the acp, it's done via an xml file you upload to the includes/xml folder - the file being called cpnav_nnnn.xml (nnnn = unique name).
In that xml file each menu group is defined and (optionally) you can set what permissions are needed to view it.
e.g.
Code:
<navgroup phrase="vbulletin_options" permissions="canadminsettings" hr="true" displayorder="10">
Almost all custom modifications do not assign any specific permissions, so anyone with acp access will see them. RPG Inferno is almost unique in not only assigning permissions, but actually creating it's own custom permission.