Fabrication processes can be patented. I can imagine examples that would be hard to definitively prove based on the final output three stages farther down the assembly line.

True, but that is the same reasoning that the law goes by when it is required to prove guilt rather than proving innocence. The legal system many times lets the bad guy walk to make sure that an innocent is not accidentally convicted or over burden by having to show innocence. Just because something criminal can happen shouldn't be enough to warrant a lawsuit. There should be proof of criminality, infringement, whatever. Otherwise the law will simply be used as a harassment tool as is being done with patents.

Sure in some cases. Don't forget that patents cover a diverse array of innovations. What exactly is being infringed upon is not always that obvious.