The Callas Blog has published an article about the necessity of «context aware” preflight. The new «Sifter» technology in Callas pdfToolbox 10 allows to analyze PDF objects in their context. See also my article A Quantum Leap in Preflight!.
Akash Choudhary describes some use cases in his post. The classic example is certainly small black text that is set to knockout:
If the black text is places over a colored background (left), overprinting is important to prevent white flashes in case of register inaccuracies in the printing machine. If the text has no background (right), it does not matter whether it is set to overprint or knockout.