As @Zetharion suggested in #620 (comment) the crafting byproduct upgrade should not expect the byproduct to be created.
The amount of byproduct items should not matter. And it should not be waited for a byproduct.

Another enhancement is to pull items at any time, but not wait for the whole crafting task to finish #393.

+1 because it is the way that Thermal Expansion do.
A bit to make compatibility with TE.

Maybe it should be achieved if crafting pipes with byproduct upgrade just acts as a filtered extract pipe, allowing only the crafting results and byproducts to be dragged. But maybe - just maybe - this is how they act at this moment. I dunno.