Yes, those are mainly third party (or in-house) applications that are attached and linked to the game engine in a sense. It's nice that Bethesda has made their own speed-tree-esque program and (hopefully) had their own face generation setup.
But yeah
Quests =/= Game engine
Faces =/= Game engine
Items =/= Game engine
Animations =/= Game engine
Models =/= game engine
And so on an so fourth. Its somewhat of an abstract topic for anyone whos not a coder, but basically the engine is the platform on which all the games content is placed... The content is the play and the engine is the theater. The game engine in practicality will really only change the hardware performance of the game, and with a newly coded engine it will give Bethesda an opportunity to include new exterior applications like Havok physics, their new speed-tree, and whatever face applciation they are using.. which is definitely good.
Gamebryo had very poor performance for it's detail of content, and a newer, cleaner engine may change that.
http://en.wikipedia.org/wiki/Game_engine:
"The core functionality typically provided by a game engine includes a rendering engine (“renderer”) for 2D or 3D graphics, a physics engine or collision detection (and collision response), sound, scripting, animation, artificial intelligence, networking, streaming, memory management, threading, localization support, and a scene graph."
The engine itself has somewhat to do with faces, in terms of face animations. But how the faces actually look, their detail and such, has indeed absolutely nothing to do with the engine.