When I Export a single file to my Desktop, Scrivener (vers 3) does not create a folder to house it. As far as I can see, Scriv only creates a containing folder when you are exporting multiple files. In short, I can’t replicate what you have described.
If you’re exporting to an ebook format, make sure you don’t have the “Save source files in a folder with exported Kindle file” checked. It’s just above the “Reset KindleGrn location” button. See the image below.
I have the same problem: a chapter in the book I am currently writing typically comprises several files (many, in fact), making use of the good advices found in the Scrivener manual.
However, once the chapter is written, I’d like to export it for spell and grammar verification and then re-import it into the binder, as, at the end, it is easier to handle (not absolutely necessary, but definitely easier).
So far, the only solution I’ve found is to compile the whole project in the Word format, delete all the unnecessary pages from the book to keep just the said chapter, make the required corrections, and then re-import the file (and move the previous files and folder outside the draft in case I need them later).
Surely, there must be a better and simpler way to do it. I am all ears.