I have finished the quest with the adra pillar, restoring it.

When I return to town, I have the talk with all the people at the harbor.

When I walk around in town then, I can take everything and it is not considered stealing any more.

 

expected behaviour:

Even if I solve the big quest, people should still not like it when I go to their house and take everything from their chests while they are looking.

Yup had the same.

 

IDK if it's expected because you've raised your reputation, or if it's an unintended side effect or raising your reputation, or unrelated entirely.