In the past this was resolved by only exercising the bounty in space that was controlled by the issuing authority. So for example, you could take a Rheinland lawful bounty against Liberty commercial ships while they were in Rheinland space, because they actually are unlawful in Rheinland. But once those ships leave Rheinland they are no longer legitimate unlawful targets and the Rheinland has no bearing.
Its the same for all of the bounties. You couldn't claim a Liberty bounty on a Liberty Rogue who is in Kusari, for example.
edit--there were exceptions to this for certain types of blanket bounties but IIRC the targets had to be unlawful for everywhere the bounty claimed to cover, and was one of the reasons why only official factions could do it.
ps--I'm not sure what is the new normal under the new rules.
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