i think the reason you can not find it is that once you remove items from the default game it does infact affect precombines. To be honest i have not ever used those precombines mods. i run a relatively light game and only have like 130 total mods, I only made this as i could not find a single mod on nexus that took and altered the terrain so that once i scrapped everything using Scrap everything mod i didnt want the dirt that washed over the roads all over as i am trying to do a clean sanctuary rebuild. I also went alil crazy by cleaning out the water and lowering the ground in it to make that deeper as well. Sure most people might not want this, but i did and i figured i would share it. The only things i deleted from the game would be 3 broken tubs, a couple boards in the water under the bridge which were not able to be deleted using any method outside of this. I do hope you find something that does what you want it to do, but sadly i do not think any mod which "cleans up" will work if you are using those precombines mods.
I like using the rebuild sanctuary mod. It does a good job in cleaning up sanctuary and the moder redid/fixed the navmesh/pre-combines. https://www.nexusmods.com/fallout4/mods/70642 Has PRP version as well
i do not think this is fully compatible with that deep clean mod, But you could try loading this after that one and see if it conflicts, i would think they do similar things thus probably not compatible
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I like using the rebuild sanctuary mod. It does a good job in cleaning up sanctuary and the moder redid/fixed the navmesh/pre-combines. https://www.nexusmods.com/fallout4/mods/70642 Has PRP version as well
Maybe in Creation Kit?