I think people tend to see bounties as ultimately resulting in the closure of their character, so they tend to see this as enforcement of a final solution. The reality of the matter is, bounties, especially first-time bounties for relatively minor offenses are almost never resultant in closure. In Dementlieu, it often results in the body being flung somewhere outside the city or in the sewers, and in Barovia it results in the Charnel House.
It becomes an issue when it becomes a repeat offense, or if the person has committed a very specific, very important crime that would merit by the DM Team's decision to see them placed in a more permanent solution, like the Gendarmerie's oubliette or the Garda's vault. Even those, with the right connections, aren't final solutions.
However, the people who put themselves at risk to pursue them almost always face recourse of some form. It's for that reason bounties are rarely pursued, and result more frequently in excessive anxiety and paranoia than they do anyone getting engaged in PvP. When I was playing a Gendarme, I think only one or two bounties were ever turned in to us across the two or three years I did it. Frequently, people out-of-character didn't want to pursue something that would result in them being attacked in retaliation whenever the bountied individual was inevitably set loose again. It becomes a catch twenty-two. The benefits to the process of exposing yourself, identifying yourself, making yourself vulnerable against a character who is already offered clemency to surrender themselves if they were going to come peacefully in the first place are non-existent. It only makes it far, far more likely that a character who is already going to face post-Resurrection retaliation from their bounty is going to end up getting killed before it's ever collected, thus never progressing the criminal case. Their only method of protecting themselves is this unfortunate process of ganking to ensure success.
These days with the disguise system, there's a chance at more anonymity with the process, but it's the anonymity that is all that protects the bounty hunters. It's a system I think could use some improvements, but mostly in the way it's executed, not the premise. I think there needs to be some kind of shackle tool that players can use on eachother that will tether another PC to them and force them to follow you, if you take them alive. The reason being that it taking anyone alive and across any measurable distance is impractical, dangerous, and if the bounty pays the same either way, not worth the effort. It's far easier to kill someone and transport their body that way. That's just how the game is.
That being said, I don't have much to add to this but to say I agree with the following posts:
Let's say I openly support or even join an organization whose mission is to rule the world and subjugate all gnomes, or ritually sacrifice the ones it does not enslave. This is an inherently antagonistic choice to make, and anyone who is sympathetic to gnomes would probably want to stop me. They might openly warn me to renounce the group, and if I do not do so, put a bounty on me.
I ask, what if the the supposed gnome killers were situated in one domain, and the gnomes in another, and do not have overlapping fields of play? Can they both exist and tell their stories without impeding one another?
Even in our world, if a criminal crosses state lines, they are not automatically immune to law enforcement coming after them. With the exception of Sithicus and Krofburg, I think most areas in the game world wouldn't care that a bounty hunter is coming in to catch a bounty from another country. The local authorities will likely think "hey, we don't want their trouble, collect the bounty. Saves us the headache." Then take it one step further with outlanders, most governments won't even think twice about a dead outlander, even more so for non-humans. In the past, I've even seen the Garda and the Gendarme making each other aware of what bounties had been posted so that they didn't accidentally aid someone who was wanted in another country.
With the association angle, authorities are likely to think that if you're friends with someone, you're likely going to get in the way if someone comes and tries to put a knife in them. If a character is aware of a conflict between two factions and willingly joins one of those factions, that in itself is opting in to the factions conflicts. When you join a faction, there's rewards and there's risks. You can't have all the good and none of the bad. If a character doesn't want conflict, maybe they shouldn't join up with a faction that is actively being antagonistic.
I disagree that it removes the right to opt out of PvP, bounties are put in place if someone opts for PvP. For example if you refuse a summons you are in fact opting for PvP. Composulary scenes would be detrimental to many players and classes hunting a criminal. While I personally prefer to offer scenes out of courtesy the very act puts the instigator at a huge disadvantage and seems illogical from an IC perspective, why would someone's character put themselves at risk to give courtesy to some criminal?
As for it furthering stories this is a persistent world, even in the worst case scenario if a character is killed and their story ends it furthers the stories of other characters involved.
Overall I do think some changes could be made to the bounty system, as nothing is perfect. I just don't think the points I addressed are the issue with the current system.
I agree with Elyan that at this time bounties do still require opt-in to PVP, it's just possible that someone who does not look at the PVP rules well enough may think they are immune to PVP.
Let's say I openly support or even join an organization whose mission is to rule the world and subjugate all gnomes, or ritually sacrifice the ones it does not enslave. This is an inherently antagonistic choice to make, and anyone who is sympathetic to gnomes would probably want to stop me. They might openly warn me to renounce the group, and if I do not do so, put a bounty on me.
If a person is bountied and feels it's unfair, it is a good idea to reach out pre-emptively to either the person who performed the bounty or to a DM, rather than to wait and hope nothing comes of it. In the case of our gnome-haters, perhaps the PC reaches out to those putting up a bounty and explains their reasons for defending gnome-murderers.
Edit: I also agree that bounties in general are good and usually pro-story. Bounties are not limited to guards, evil PCs and the underworld can and do put out bounties as well.