How does this work with the scrapping system? A mod like Scrap Everything would be causing problems everywhere- wouldn't it? Must have disabled pre-combination like you said. I don't use the mod myself as I had heard of issues. I use something similar though that sets up a workshop area anywhere. Like you said adding to world-space seems to work fine. But scrapping outside intended areas causes problems and sometimes CTDs. The amount of variables to consider for altering a significant amount of content is staggering to say the least.....and then in combination with a rather lengthy load list it is a wonder that the game works at all. If nothing else, the game is certainly more stable than say Skyrim.
You can't scrap a precombined object (and many precombined objects have associated occlusion data stored in the .uvd file), so Scrap Everything (and Spring Cleaning before it) just disables it, but only for the cells in (or near, for previs) the vanilla/DLC settlement cells. The only problem this causes (for exterior cells) are to be expected when you disable performance optimization measures (i.e. reduced performance, mainly only noticeable for Bunker Hill and to a lesser extent Hangman's Alley). This means no occlusion issues, and the only mods you'd need to make a patch for are the aforementioned lighting mods. For everything else, it acts as a sort of lazy compatibility patch.
You do want to be careful scrapping in Hangman's Alley though, Bethesda didn't really make a full landscape there, so scrapping certain parts of the surrounding buildings will let you see below the ground (to the secondary ground layer far below). No weird trailing like you get with the Void though.
And, as mentioned before, disabling previs reveals Bethesda's lazy room bounds/portals system underneath, so for interior cells you have to either regen the previs or fix the room bounds/portals. SE's first attempt at regening previs/precombineds for the interior DLC settlements seems to be hit or miss (works for some, not for others), but we will be attempting to fix that once we get the other planned features working.