While Kingpin offers it in the first conversation, he immediately turns hostile (along with the rest of the whole PIN faction) on second visit (just by talking to him again immediately, or waiting a few seconds). When I cheated, added the MOC list item and gave it to him during the first conversation quickly, the quest worked - he gave me the money, even mentioning a certain newspaper editor he'd like to get rid of. The MOC list remains in his inventory, so theoretically the player could kill him afterwards to get it again, just with the original JA2 campaign Kingpin (the chalice double-cross).
(it might also be a bug with one of the PIN guards patrolling the halls nearby one turns hostile after a while, which might have initiated it all - perhaps an AI issue with aggressive + on guard set for them?)

She was kept in prison level under the Port Kip police station (not in the aboveground cell) in my playthrough, meaning that any "stealth" rescue with blowing up the police station wall is impossible. I guess that's on purpose, since the aboveground police station has additional alarm triggers where the wall people used to blew up is. But That makes completing this quest one of the first players encounter, if they enter Port Kip as first or second city (which is probable, being so close to start) initiate hostilities with the whole PIN group, which is IMHO pretty premature at this point in the game. New players would end up aggroing the whole PIN faction right from the start and miss out on dialogue, quartermaster trader and possibly others.

Possibility of stealth rescue or something like that would be really nice, but not sure how to go about it. Perhaps by adding exit grids to the (nonfunctional) elevator in the police building and one in the basement and changing few guards near the cell to a different faction so they could be taken out safely by stealth (just killing one PIN guard stealthily still aggros them all, and that can't be changed without breaking other things).

GR are a civilian faction that's initially neutral, unless players steal from them or wander into their sectors at night. Which is right as smugglers, they initially profit from player's buying of weapons at Tony's (even though most players will turn on them sooner or later)

Unfortunately, several named GR NPCs have a wrong faction set in the map files instead of set to civilian (GR), they are set to enemy faction. Meaning they shoot on sight, meaning player kills them, making them all hostile everywhere.
That includes their leader Walter Smirnoff in K14, who the player is told to contact by several barmans and neutral GR NPCs. Making him neutral by map editing shows that he has some unique dialogue lines, although that's it.
The bugged hostile ones, named "Gun Runne", are in D1, I16, B16 (MercProfile.xml IDs 152,154,199) and of course Smirnoff himself in K14 (ID 73).

Talking to locals in C13 Calisto should give you a quest to "Take care of Lynn in Calisto (she's the factory manager using child labour as in original JA2).
Broken because she is again placed on the map as an enemy, not a civilian (she should belong to Crepaton faction, initially neutral). So she attacks the player on sight as they liberate Calisto, but she should be initially neutral I think. Therefore the quest completes ("Killed Lynn") even before the player is given the quest, without a chance to see any dialogue.

Broken dialogue? After editing the map to place her as correct civilian and being given the quest to take care of her form the liberated locals, she just says over and over "Not now, you are a walking target, in case you haven't noticed" like if one tries to talk to other named NPCs during combat. But the whole town is liberated, obviously. Finally, on wounding her, she has the rest of her dialogue lines, then attacks.

Player is told by locals that Bruno Stolitz, leader of the gangsters Satan's Sons, is hiding in Drake (H3) basement IIRC its I3, basement lvl. 3.
Polish mission FAQ mentions Martha and that Bruno is in fact her "missing" son "Joey" (from the original JA2). Martha should give player a quest to rescue Bruno/Joey and escort him back. However, Martha is missing from the game - she should appear in G15, but her CivGroup is set to None in MercProfiles.xml and she is not placed in the map file. She is still in sector scripts though, as on entering G15 you get a "Noticed someone" NPC notification.

Editing her and placing her on map results in broken dialogue and a broken quest:
First she says the lines that she's supposed to say after you bring Bruno/Joey to her (she apparently shoots him for not being a nice boy like she thought, but an evil gang leader). Bruno/Joey gets deleted from game, even if you haven't even met him yet...
Afterwards, she says the lines that should be first, that "her son Joey is missing, please rescue him" and gives you the quest to find (deleted) Bruno/Joey.
Seeing Bruno first without talking to Martha doesn't work either.

No idea if this quest was just scratched from the mod or left unfinished, but the mention of it in the old UC FAQ and the NPC notification on entering G15 makes it look like a bug.

DNP faction is initially neutral, even though they are a corrupt police force that player should eradicate. But on most city maps with a police station, there is a bright-blue NPC police chief, which is hostile to you on sight.
Map files shows he is placed as enemy, even though DNP is a civilian faction. Killing him when he attacks you on sight obviously makes the whole police force hostile. This might be as intended, though, as a script-less way to aggro the police in the city? Still, it's very unclear what happens. Player sees a hostile guy near a station full of neutral police, obviously kills him and all police turn on him...

Carmen gives you the quest to hunt down Crepaton managers and bring him their heads. Like the terrorists in JA2, these are randomly placed. Unlike original JA2 terrorists, these are set to Crepaton CivGroup and have AddToBattle=1, so whenever a player kills one (including Lynn, the factory manager), all others - whenever they are - turn hostile. This can make it very easy to miss them in the heat of battle, as they are all in city sectors, as they show up as normal enemy hostiles (albeit with the ??? NPC mark), so a player might miss them and either kill them by headshot (ruining the head item for Carmen) or just forget where the body was. In JA2, I usually used spies to eliminate the terrorists silently, even way before taking the sector (it's a nice source of free income).