Not gonna lie chief, don't fully know what pre combined are, i'm a huge novice in the creation kit, literally just doing this to remove stuff for a friend. Things outside of the existing build border will possibly be done, maybe in an optional file.
A precombine is basically a really big mesh that combines different objects in one cell. For example instead of rendering a tree group, the pile of rubble and the stones besides them as seperate objects the game combines them into one mesh and needs only to render the visible parts. The precombines untouched give you a much better performance. Less stuff to render = better. If they are broken (which is very easy to do in CK) the performance will suffer a lot and ctd can happen. You need to rebuild precombines if you want to avoid problems. Never delete any vanilla reference. If you wanna get rid of Rubble Piles etc. it´s better to move them under the map, because this can cause ctd to. I started new and get rid of scrap everything and mods like morexplore because they break precombines. Now I have a much better performance.
This is basically what I do now. I use Place Everywhere to lower an object until there's just enough showing for one more move, then give it another shot to shove it down into the ground. It's still there but out of the way. Getting rid of all the crud manually is a pain in the ass for sure, especially given Bethesda's propensity for creating massive piles of rubble and junk in places where there's no plausible reason for it being there but your game will be a lot more stable if you either leave the precombines intact or rebuild them as you go.
Regards precombines, whilst the resultant issue of "breaking" them sounds bad and is the focus of folk's ire, they aren't really the cause of the problem. The real culprit to me seems to be game/cell design. For example, precombine meshes could've been made smaller or more selective, compromising some FPS but focusing on making the game easier to mod. The underlying culprit is probably because the game is built as a console port. Maybe whenever folk say "breaks" precombines they already know all this, but I fear come hear the word "breaks" and don't realise the real problem is the sh*tty porting - and rotten game design. I mean, who designs a ruined detailed city where almost all the effing doors/buildings are sealed? And then makes it difficult to cure with mods? Multi-platform, money-grabbing, console-porting game companies, that's who.
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What about stuff outside of the build border for existing locations? Trees and other junk that blocks perimeter turret range?
Never delete any vanilla reference. If you wanna get rid of Rubble Piles etc. it´s better to move them under the map, because this can cause ctd to. I started new and get rid of scrap everything and mods like morexplore because they break precombines. Now I have a much better performance.