If you are in the jurisdiction you want to bounty hunt in, then you don't need the KWS. Just do a normal scan to see if they are wanted in the system. Attack then hand in your bounties as normal. If you are a bounty Hunter, I have to assume you don't care about the BGS so the new version looks good for bounty hunting.
Sorry, but I see no issues here.
Maybe this will help..
System ruled by independent Faction A, but has imperial factions B,C,D and E
CG says Faction A wants to get rid of pirates.
Ship 1 belongs to Faction C, but highest value is for Faction A. it has also bounties from Faction C
Old system, you get faction A rewards, but also Faction C likes you a little more as you got rid of someone they wanted dead. The empire also likes you a little more as faction C is imperial
New system(3.0 beta), you get faction A rewards but now Faction C likes you less because you blew up one it's members, as does the empire.
You decide the CG system isn't working well. so you move to system ran by Faction D, which has a haz res
Ship 2. Belongs to faction D and the highest value belongs to Faction D. BUT it also has bounties belonging to faction C
Old system you get something to go towards the CG, new ship you don't as Faction D is greater.
In addition, having the best way to achieve a bounty hunting goal by not carrying a bounty hunting device seems a little... odd.