For example Karma is disabled in Admin -> Core Features. You go to action=admin;area=featuresettings;sa=karma you will see the karma settings page (which might be OK now), but of course none of the menus are marked as active since Karma doesn't show up in settings tab. Now enable karma in this page; of course successfully enables and starts working; but Karma is still disabled in Core Features section and therefore still doesn't show up in settings tabs.
Probably no-one will go to settings using direct URLs but a bug is a bug; because for example if you installed a modification that redirects you to a disabled core features settings page and you enable it; you will never be able to find that settings page again unless it's enabled in core features.
Sum up: Disabling a core feature in Core Features page disables the feature correctfully, but enabling it in it's page won't enable in Core Features page.