Most of what's in Setting is really just a new overlay over the old, existing control panel is what I'm saying. Another way to 'get to' the same place IOW. Somewhat like the way Google.com is the same place whether you get there via Chrome or Firefox.
And I tend to agree about Skype ... in an ideal world ... but there's a few reasons why the ideal thing may not happen.
Sometimes if a Developer makes an app (App 1) that installs another app that already exists in Windows (App 2, something like Skype) they do so because the App 2 version they installed is customized in some way so that it supports App 1 fully.
This also makes it so PC's w/o App 2 already on them (someone still running W7 or even XP may not have Skype as it's a relatively new add to Windows) will reliably have it, so that App 1 can always access it.
App 1 installing it's own copy of App 2 also allows the Dev to control the versioning of both App 1 and App 2 at the same time, they're not reliant on the whims of Microsoft Windows team, who could, say, suddenly take away support for some feature of the built-in version App 2, thus breaking features in App 1.
Another scenario: App 1 was developed before all PC's had App 2, and App 1 has just never been updated to account for this fact. It doesn't even 'know to look' for a built in copy, it just puts it's own on there, period.