This may be an unintended behavior Reply-Rules bug, but this is what's happening:
1. Group setting (and membership) is set to unmoderated.
2. A particular topic (TopicOLD) is manually set to moderated by the mod.
3. A user pulls the old "too lazy to create a new topic" switcheroo and they click on Reply to one of those (now moderated) TopicOLD messages, either through email or online, changes the subject to a new one, adds the text, and sends it as a "new" to them topic, but which as we know now contains the In-Reply-To: entry referencing a message which now points to a moderated topic.
4. When the message is parsed, the new-topic subject rules are applied but it seems the in-reply-to rules are also applied.
5. This causes the message to correctly create a new topic (TopicNEW) which technically should not be moderated as it's a new topic, but the message still ends up in the pending queue.
PS: The above is the "consistent" problem/bug behavior. It then got a bit weird while testing but it seems it's some sort of Thunderbird-specific behavior, I don't know, but I included it here just in case. I may retest this part with a different Tbird version later on.
6. As expected, after I approved the pending TopicNEW topic starter it got created as a new topic, not moderated.
7. If I reply to that 1st TopicNEW message through Tbird (without changing anything) the reply still goes into moderation, consistently for all the times I tried replying to that 1st message.
8. If I reply through Gmail or online to that 1st TopicNEW message, no problems.
9. If I reply to any other message but the 1st from TopicNEW through Tbird, no problems.