If that ever happened I would be quite pissed.
My biped uses the dragon stoneworking (for making bricks) since that puts him at 3:1 on them. There's no masonry skill there tho, hence still a need for a biped stoneworking hut.
The skills from crafting machines are all working as intended. The only thing that might not fit is scaleforge cannot craft armor or weapons for bipeds. If the design is sufficiently different then this probably makes sense.
The skills that get no bonus period were done that way on purpose: Example some of the formulas for RoP require transmuting skill but the item is crafted at a stoneworking pedestal. There's no possible way to get a shop bonus. This was intentional.
The ONLY change I can see advocating is taking away an Anvil's ability to make scales, OR adding anvils function to a scaleforge (minus any skill bonus obviously). And really this would be a waste of dev's time.
/move along