Well, I agree in the planning ahead thing, only sometimes timeframes are crazy enough so you don’t really have time to plan before prototyping.
I usually end up with what i call the “Undead Starter Content” directory.
I delete actors referencing it, I delete meshes, materials, textures (in that order), then save, exit editor, manually delete directories in project, reopen editor and BAM, here’s the starter content dir again.
Then i redo everything again, usually on the 4-5th try of doing the same the engine is done and actually stops recreating it.
Only then for whatever reason i delete the intermediate and saved folders (only one ssd on this machine i’m using now) to make some space on the hd and after opening here’s the undead rising!
It would be funny if only I was always sure of project integrity. Problem is that sometimes you lose everything, especially if you’re as stupid as me and don’t do backups. Ever. 
I agree with Hyperloop though, content structure should be decoupled from actual filesystem.
Unreal is in this middle ground in which it manages everything but only up to a certain point. I’d rather do it all on my own or be completely managed. Second option would be most benefical to me.