Breaking into houses to complete quests in a city in the grips of a tyrant is perfect neutral good roleplay. Taking stuff marked in red? No, that would be chaotic action and I were DM I want to hear why its consistent with your understanding of alignment.
I'm not surprised that the game tracks things like this - the Larian CEO has said that Ultima was the game that got him into cRPGs and that game tracked each time the Avatar stole things.
