Whether or not you can claim a bounty on someone and whether or not you can actively attack them are two different matters. If you're using a faction ID, the restrictions on whom you can actively attack is defined in your ID, but once the fella is dead, you can claim it regardless of whether it was an engagement by you or a mere case of self-defense.
To use the example in the thread you linked, Daumann ID allows attacking Hessians, so if you run into a Hessian you can start the engagement within your ZoI, and once you've got the kill, you can claim it on the boards you're registered to. On the other hand, if you run into a Unioner, since your ID does not allow you to initiate the engagement, you can only act in self-defense, but again, once you've got the kill you can claim it on the boards you're registered to no matter who shot first.
