I don't think you can say that unless you have a very deep insight into how things are counted. For all we know the old system is completely rewritten to accommodate the new C&P system and old system wouldn't work any more, even if you wanted it to.
Instinctively I wouldn't want to use two systems either anyway though. In fact two systems like a REALLY BAD idea to me - a bug fest. Better to use the same C&P system for both .. and if necessary adjust influence + cred score generated on NPC's to reflect the fact they're not persistent like players are .. and adjust for the PvE gameplaying fact that a KWS scanned NPC has X% fewer bounties on it in Beyond Chapter 1. If each bounty pays X% more though, then what's the diff?
What I think IS a fair point is that local faction influence changes should be a yellow flag, just to double check that killing NPC's doesn't have unduly bigger effect on the BGS than killing players does, and vice versa.
So what you are saying is the system redesign for crime and punishement (which is already overcomplicated and all most wanted was bigger fines and tougher cops) somehow prevents the KWS looking up all bounties stored on a DB for someone/NPC?
Because if that is what you are saying that would be insanely bad! That would be a monumental design failure from the devs....
Me I chose to believe it's choice by the devs mixed in with a bit of ignorance of how people use the KWS...but if you want to say it's because the devs messed it up so much what should be a simple SQL query is now impossible then far be it from me to get in the way!