I've been playing Fallout 4 recently with the Conquest - Build New Settlements mod, and combination with mods like "Scrap Everything", I've discovered some interesting trivia about the game world.
The mod allows the player to literally build anywhere the player can plop down a workbench, even in interior areas, which means the player can pretty much rip down the world (especially with the Scrap Everything mod, though some objects are still not covered) to almost nothing save the bare ground.
However, I have discovered some things to keep in mind and some issues that can occur if you these mods.
* You can break the ability to ever have Codsworth join up with you if you use the Scrap Everything to scrap all the Radroaches and Bloatflies in Sanctuary, BEFORE you either tell him Shaun is missing and you checked Sanctuary, or before he accompanies you to look through Sanctuary and comes to that conclusion himself. The game scripting is dependent on the living and/or dead bodies of the monsters to be present because they allow the game scripting to progress the dialogue tree, serving as control switches. So, if you kill the bugs, then talk to Codsworth, the game will register the dead bodies as being present in the game world and present the option to tell Codsworth you checked those locations already, since he goes with you if you haven't and will help you kill them instead. It's safe to remove them from the game world via scrapping or the console with the "disable" command AFTER this has occurred, before will break the game quest logic. This can also break quests in other areas, so make sure you've not removed corpses until after their intended quest purpose is over.
* In general, scrapping corpses can and in most cases will prevent their re-spawning in many areas, so be careful if you use these mods, since you can even remove monsters before they appear (in the game engine, they have invisible placement triggers that spawn them that some scrapping mods allow you to remove), so if you want to kill them again when they re-spawn for more loot when the cell refreshes its contents, don't scrap the bodies. This also applies to items you can find as well as containers, scrapping them will prevent them from ever re-spawning, so pick up the items manually or place them in the workbench when using the Conquest mod.
Exterior cells, unless they are too close to another settlement's crafting radius, these can be scrapped down to nothing if you so choose, but this can lead to some issues.
* The game makes frequent use of "culling", a graphical trick the game engine uses to save VRAM. This means if certain areas are never meant to be seen from certain angles by the player, they will be "culled" from display from that angle, saving VRAM and processing cycles. Unfortunately, these mods allow scrapping objects that block culled areas, which can cause these areas to freak out and the game world will appear to blink out of existence while walking through these areas. This can be disabled to a degree with tweaks to the game INI file, but a more efficient solution is to create a mod that adds a checkmark to disable culling in the affected cells. This has it's own problems since you must apply this checkmark to all cells loaded around the affected game cell, and while some mods exist to do this to a limited degree, this can cause the average gamer issues in areas not addressed by a culling disabler mod (which needs to load dead last in your load order to work)
* Another related issue is that scrapping certain objects in exterior cells can leave literal holes in the game world. For instance, scrapping the huge rocks around the Quarry Excavations area will leave some nightmarishly huge holes in the world itself, which the rocks filled in. This can be ameliorated somewhat with mods that allow the player to re-add landscaping objects to the world, but sometimes you can't place objects to fill the holes. Thankfully, if using the Conquest mod, it makes a save file by default every time you set up or remove a workbench, so just go back in time if you leave a game world hole and remember to leave those objects unscrapped next time.
* Interior areas are even more bizarre. Some objects are expected to exist in a cell, and their removal will not only result in culling issues, the player will experience the world going white in the affected areas. Disabling the culling in these cells does not address the problem like it does in exteriors, which means a modder would have to manually edit these cells to fix this.
* Generally, you can scrap small objects, most trees, cars and some wall and ground decor with no problems. Scrapping entire building sections can result in culling issues, especially if the objects were never originally intended to be scrappable. Again, some mods fix these issues, hunt them down before you go nuts ripping the world apart with a workbench.
* Another rule of thumb: Some objects just cannot be scrapped. Some are part of "static collections", which are a bunch of meshes and textures grouped together, and the only way to remove some of these is via the console "disable" command. Also, some objects cannot be relocated or moved around without the Place Everywhere mod, which I highly recommend if seeing things like objects hanging sideways in midair just drives your sense of feng shui crazy.
* A curious thing I've noticed is that in some areas you can't place a workbench on bare ground, though you can on top of a scrappable object like a debris decal or trash pile. This is likely because the workbench requires a solid mesh to sit on, and since some areas are literally blank space underneath the ground texture, the game is reluctant to plop down the Workbench because it could fall through the floor. This is particularly prevalent in interior areas. Oddly, if you scrap the object the workbench sat on, it will automatically fall to the ground and stay there like it would normally.
* A final rule: I highly recommend a mod that makes junk weigh nothing if you compulsively use this mod, because everything you scrap that returns a resource will have weight, and you will wind up having to carry it all the second you remove a workbench.