I can't believe I never noticed this on my own, thank you for telling me.
It wasn't cleaning up at all. I was performing a validity check on the decorative scan results - but they don't have a "valid" property. So when I checked for it, it came back nil, which compares as false in boolean logic. So every single time it tried to delete a decorative it was aborting at the last moment because I wrote the mod to not perform the deletion if it was invalid.
And the worst part is that I never needed to check for decorative validity. They don't track it. Decoratives aren't objects. There can't be an invalid reference because the game doesn't provide a reference for decoratives - you just get the coordinates of where it is and the type it belongs to. You have to tell the game to perform a deletion at those coordinates. If there was a decorative there and now there isn't, it just ends up deleting nothing, not crashing horribly like it would for an entity.
This mod. Since version 4.0.0. Has been doing nothing.
And you're the first person to notice. Before any other player; before the lunatic in the other thread who finished a playthrough in 3 days; before me, the author and tester, who has literally looked at it not clearing creep patches and thought to myself "Wow I'm getting really unlucky on these coordinate rolls, but it's fine, it'll get it eventually".
I'm a moron, you're a hero, and I'm pushing a fix for this most heinous bug in a moment, along with the "clean here" command I used for testing and the "clean everywhere" command you asked for. The other stuff will hopefully come later. Thank you.