So, it seems that any change of subject on a message posted by email will start a new topic.I think you misunderstood what the issue is. The new topic creation part works fine and as expected, since the subject was changed. (to a unique one)
Assuming the code order of evaluation in the threading algorithm is as described in the doc:
1a. The reply rules check is (correctly) performed because the message headers contain the In-Reply-To entry and it references an existing previous topic (which happened to be moderated in this case) ...
1b. .. and the subject check is then performed but since it's different, the algorithm now correctly creates a new topic.
2. However, the code also inadvertently inherits/applies the moderated property of the aforementioned referenced previous topic ID; or alternatively it doesn't reset/clear the mod property for the new topic, which is the bug, it causes a brand new topic to inherit the moderated property of a previous topic when there shouldn't be any association to the old topic since it's a new topic. (not sure if it also inherits anything else besides the moderated property)
It's one of those bugs that will only show under certain circumstances, under normal conditions in an unmoderated group if nothing gets moderated no one will know. It only showed up because I specifically moderated a topic to (gently) end discussion on it (without locking it) and someone used a message from that thread but also changed the subject so they can create a new topic, causing the new topic to be moderated. If I hadn't moderated that previous topic I'd have no clue this is happening.