Frankly, the various PDFCS should not be treating every salvo separately. They should instead check salvos on the basis of 'am I authorized to engage' (ie, is the salvo hostile or friendly), 'is the target in range' (for Area Defence PD), 'is it targeting my TF' (for Final Defensive Fire) and 'is it targeting me' (for Final Defensive Fire (Self Only)). It should then generate a list of its own (or for less calculation requirements I'd expect generate a list for the TF with all Area Defence PD, TF-wide FDF and ship specific FDF(SO) PDFCS and weapons) and start shooting, treating every category list as one big salvo.
Yes, this means that some big salvos might get lucky and not get engaged and thus turn their targets into expanding clouds of debris. That'd also happen in reality.