Scrap Everything disables previs and precombineds in the vanilla settlement cells in order to let you scrap everything*. If you use an expanded settlement mod (or a mod-added settlement) and have a ton of things you can't scrap, you'll need to apply those same edits. Note: any cell already edited by Scrap Everything will have a yellow (or red, if you have a third mod making different edits to the same cell) background.

For editing it yourself, it's pretty easy to find the relevant record:
1) In-game, open the console and click on the thing you want to make unscrappable***
2) Launch FO4Edit (I recommend deselecting all plugins but the SE plugins)
3) Search that FormID
4) Go up to the Cell it is contained within (Just hit the left key twice)
5) Copy as Override that record into a new plugin**. DO NOT use "Deep Copy as Override"
5a) If you are doing multiple cells (very likely), repeat that process for the rest of the cells***
6) Clear the following fields from all the cells you want the edit applied to. You can do this two ways:
6a) Use this FO4Edit script**** to automatically apply the necessary edits to all the cells at once

6b) Manually: Must be done for your created plugin, not Fallout4.esm (it won't let you directly edit Fallout4.esm). 
7b) Right Click -> Remove  on the fields for VISI, RVIS, PCMB, XPRI, and XCRI. Do this for each cell.

Then save your plugin with whatever name you want. If you want to merge the edits into Scrap Everything, select all the newly edited cells (from within your plugin, not Fallout4.esm) and use Copy as Override and select the Scrap Everything plugin you are copying them into. 

*Check out this thread for an explanation of why.

**You can copy into the Scrap Everything plugin, but I recommend making a separate plugin first even if you want to eventually copy the edits into Scrap Everything to reduce plugin count. That way you can easily copy the edits back in when Scrap Everything updates.

***Not sure the best way to figure out all the ones you need, it's hard to judge the boundaries of exterior cells. To give an example, Sanctuary is roughly 10 cells. The quickest way would be to include the neighbouring cells (FO4Edit lists the coordinates of cells, so <8,12> is "west" of <9,12>, and north of <8,11>). Doing that for the cells immediately around one found just at the edge of the vanilla bounds (i.e. near the "first" large thing you can't scrap) should work fairly well, and won't result in too many unnecessary edits. One thing to note, previs/precombineds are a performance optimization method, so if you already have a performance impact from SE, be careful making too many more edits near the cells you are noticing the performance impact around. 

****
0) Download the linked script, and put it in your "Edit Scripts" folder in the base game folder (the one with Fallout4.exe in it). Because it doesn't go in your data folder, it must be installed manually
1) Launch FO4Edit (let it load your regular load order)
2) Right Click the plugin -> Apply Script -> EXT Worldspaces Pre Vis Disable xEdit script.pas