I'm going to do some proper testing of this to actually nail down how it works but my initial testing has shown that, and I will confirm this if I can,
the target having a bounty or not is entirely random.
I'm going to run some more scenarios but this is what I've found so far (to be continued):
1. You can take a "legal" take down, they flee to an "illegal" location, you profile scan them, they
don't have a bounty (
you get a bounty)
2. You can take a "legal" take down, they flee to an "illegal" location, you profile scan them, they
do have a bounty (
you don't get a bounty)
Deductions so far based on this:
1. The target location in both cases was owned by a legal faction, so the owning faction of the target location has no bearing on the fleeing target having a bounty.
That's all I can deduce so far.
What I'm going to test:
1. All of the above but you kill the target,
then profile scan them (to see if you get a bounty or not, whether scanning is essential or not - this may require a lot of tests and a lot of bounties on me

)
2. All of the above but you find them at an anarchy owned location (and this might take a very long time to actually get to happen), try killing them without a scan.
3. Try to find a bounty target via profile scan at a non-anarchy settlement and kill them.
4. Potentially do the same but scan after kills. I may not bother with this one though, depending on the outcome of earlier tests.
What I'm hoping to deduce:
1. For a fleeing target, is it essential to profile scan them first?
2. And so, is it the profile scan revealing the bounty that removes illegality of the kill? Or is it the bounty?
3. Maybe, though unlikely, can we control the fact they have a bounty or not to avoid the illegal outcome of this mission type? For this, I'd need to spot a pattern with the targets who do have a bounty, so this is up in the air.
4. Does profile scanning to reveal a bounty negate a penalty in a non-anarchy location? (some might already have the answer to this but I'd prefer to find out myself)
If the conclusion is the profile scanner is the way to avoid penalties if the target is a criminal... why did FD decide on foot would work so wildly differently to in ship?
I'm fortunate that my home/colony has an IF contact that I can use to clean these bounties immediately (due to no notoriety for these missions). I prefer not to take them but when I was hunting materials... sometimes those 15+ manufacturing instructions can't be passed up. What I'd prefer is if the mission says it's legal, the target should automatically
always have a bounty. Because then I'd like doing these missions a lot.
To make my point clear, this is what I think is messed up (I'd be fine with needing to scan a fleeing target first... I'd be miffed by the inconsistency of it, but I'd accept it... What I don't accept as intended is these literal bounty hunting targets not having a bounty - this directly contradicts how the ship versions of these missions work - you never, ever, get penalised for killing a legal take down target, irrespective of the location).
Just to be clear for anyone new who may be reading all this, a target doesn't normally have to have a bounty for you to cleanly kill them in a settlement that is owned by an anarchy faction. Some have a bounty, some don't. You get no penalty (scanning them or not) because the location itself has no law. This has been long known. This is why I never thought the profile scanner had anything to do with it. Indeed, there is no scenario outside of the fleeing take down missions (and nowadays, I think, the PP2.0 agents?) where it's even possible to find a mix of anarchy and non-anarchy targets in any location. They're always the same faction (I don't include the protect missions, legality has no bearing there, just like CZs). And whenever, wherever, you find scavengers, they're
always a criminal faction - you can
always kill them,
no penalty, no need to scan them first (in fact, scanning them after the fact rewards you nothing, you get the bounty on kill). It doesn't matter where they are.
So why isn't that the case for these literal criminals we're hunting?
It is... just too confusing for the average player and I wish FD had fully fleshed this out early on.