Argh.
Already, without writing a single line of extra code, permissions can be set for specific features outside the permissions area.
Grab an SMF forum. Doesn't matter what version (though if it's 2.0, be sure to turn the calendar on), then go to the calendar settings. In there, there is a collection of permissions for the calendar.
You don't even have to revisit the permissions page to set them, you just configure the calendar right there, its settings and its permissions.
Now imagine that the calendar is a plugin. It will be eventually but right now that's hypothetical. Anyway, the calendar is a plugin, you enable it, an icon appears in the Plugins area in the ACP (menu included), where all the settings are.
My central point is that if you are defining a page in the admin for something, why is there a need to put part of its configuration in one place and part in another? Especially when it is not immediately obvious what is going on and causes so many questions for users.
This lead me to wonder if, in fact, it would be better not to allow the main permissions to be directly configurable and force plugins to contain all their permissions in their own configuration area.
There are not that many cases where a plugin would add a permission and no other settings whatsoever, in fact I can only think of about 3 cases I've seen where it would come up and even then, it still requires more work than just setting up a permission anyway.
I would note that plugins having their own permissions/settings area is not unheard of, nor is it unheard of to force them to do that. WordPress operates on that sort of principle, as does iOS, and for good reason.