When the job block of a villager is underground (for me it's just 1 block of earth above them), after the shift, they get stuck in the corner that is the nearest from their bed in block coordinates and don't seek the path through the door opening (1x2) that is 10 or so blocks in the opposite direction.

There is no problem with this above the surface.
It's like the priority check for opportunity to pathfind is on vertical and not horizontal.