Where is the UE5.6 MetaHuman's skeleton?

This happens because body mesh geometry that is hidden by the clothes are removed for performance reasons. But you should be able to animate the full MetaHuman in Sequencer by dragging the MetaHuman blueprint to it.

The Face follows the Body, so you can apply a single Animation Sequence to the Body and the Face should follow. If the animation sequence in question has both body and facial animation curves the values are going to be piped to the correct skeletal mesh.

I will recommend for you to watch the talk MetaHuman Animator in Real-Time where you can learn more about to play animation into MetaHumans