Oh, I just tried that out. You can indeed drag & drop between 2 nautilus windows, if you have them already side to side. You cannot switch to the window with alt/super+whatever while dragging though.
Now I also tested the same thing with nautilus and pdfsam. You can also drag & drop a pdf file from nautilus to pdfsam if you first move the nautilus windows beneath or partly over the pdfsam window so that you can drag & drop the file.
Oh Lord, so now I have to rearrange the windows before I can drag & drop a file.