What is hook_menu_alter used for? In simple terms, what is hook_menu_alter for? I understand callbacks in general, but I'm not quite sure if this method is misnamed in a sense, as I see it used in the context of permissions rather than menus. I'm probably just confused.
I think that your confusion comes from the fact that Drupal 6 and 7 mixes menu and routing. One set of hooks for both purposes, and here you have problems. If this hook was named hook_route_alter(), using it to alter permissions to some routes would be obvious, right? So that's what modules do, using the name they got. Personally I agree it's not most lucky naming, but once you remember that in this context, basically, menu == routing, it all becomes much more intuitive.