It would seem the vertices of the joint are too high to smoothly transition across the joint with auto-skinning, you could either weightpaint the vertices or simply move them like this:-
Hi, have you considered adding a subdivision modifier after the armature, this will smooth out a lot. The alternative to using shape keys is to use more bones, if there is one bone per edge-loop then you will have total control over the curvature, though it makes animating more complicated, but it all depends on what you’re trying to achieve for final output.
Maybe I’m odd for thinking of a different approach, but perhaps a bendy-bone that spans the length of the intermediate joint section? Or does that complicate it too much? (As it may need some meta-rig stuff to constrain and preserve a general pivot area.)
