My impression is that the 3D modeling in the Blender version has many things that are too small and/or detailed for the output resolution, and therefore look quite bad, whereas the hand drawn version prioritizes clean pixels and readable shapes at the expense of "realism":

  - the rims of the stacked drinking cups
  - the rims of the stacked plates
  - the filling of the pie
  - the shadows under the plates, the pie and the mini-billboard

Some objects in the Blender version are also a bit off regardless of the output resolution, for example the huge pipe and the wide forks.

I think more iterations of improvement on the Blender version would have allowed results close to the hand drawn version or even better.

For producing many 1-bit illustrations of this kind for a whole game, mixed techniques are probably the best path: retouching imperfect NPR renderings, assembling drawn and rendered elements in an image editor, using pixel art as a reference for Blender and hand-drawn sketches as a reference for both drawing and 3D models, applying filters to photographs, and so on.

It’s just the artist’s opinion. They were going for something, and the blender-rendered version was not it. When it comes to stylized graphics, there’s no such thing as “better”

The hand-drawn version feels less "mechanical" to me. It's hard to explain, but it's like watching an anime where the artists switch from 2d to 3d animation for complex or repetitive scenes in a way that feels cheap or jarring.