Okay, I tested it again. And again, the guard in the port can be looted just fine, and I chose another spot to kill him. Then I went to the back of Philipsburg and fought them lazy soldiers walking around and all is well with the looting and stuff, their ally cannoneer even fires at me but those two dumb gate guards won't fight me in the middle of all that racket but I myself can't deal damage to them in return. They have a different uniform, so I guess they only care for others with their same type of uniform.If you had seen my pictures exactly or my savegame loaded you would have noticed that I meant other places in and around Philipsburg.
TAL:
EDIT1: I also killed several hostile townfolks inside and out the town and all seems to work just fine.
EDIT2: No disappearing corpses btw. But Corpse Mode 3 dissolves the corpse(s) after looting.
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