First off, how can you punish a topic? They don't have interests, desires, sensation, or cognition.
It doesn't punish a topic. Say you have four links all carrying the same AP story. We can remove three of those. If we have five links asking about aliens and Christianity which are thematically the same, the one with either the most posts or best posts could be left up while the others could be removed. If the AP stories each contained additional information they could all be up and if the links about aliens and Christianity asked different questions they would also be fine. But I'd also probably cite this policy if I saw 10 submissions with the same title as well, and actually may have cited its predecessor once upon a time for that reason.
Inasmuch as this is an unsupported assertion, the fact that we have the opposite intuition has to ultimately count for something.
One instance that we make exceptions for are holidays, especially religious holidays. We also have eased back following major elections and other times as well when major news happens. Our timing may be off one way or the other on when we begin to return to normal but we conscientiously pick our battles on this because sometimes we shouldn't enforce it.
I'm sure we'd all love to hear reasons for that rather than edicts.
Sometimes multiple submissions for the same story will contain multiple conversations of a really high caliber. I'd rather be able to let them stay if I come across it late.
How are we to know which are rules and which aren't?
I have tried to clarify things as I can with this which is linked to in the XP in various places. I have also invited other moderators to add to this as they find the opportunity. But the policy on repetitious posts is the last on the list of bannability. It's about tidying up rather than being punitive. The only time it might result in ban is if one user posts the same thing on purpose over and over again. There would probably be lower hanging fruit to refer to instead though instead of the specific point on repetitious posts.