Most of this can be taken care of by using "Save to disk in a single directory" and/or configuring the output templates.
Save to disc in a single directory will just save the book file, after writing the metadata into it.
Or you can configure yours in Preferences -> Import/Export -> Saving books to disk.
https://manual.calibre-ebook.com/template_lang.html will tell you more about how to write a save template that names the files exactly as you wish, but you can probably figure it out from the lower panel. If your template doesn't have / in it, it won't create sub-directories. That is also where you can turn off the opf and cover file.
phossler's post in #3 is essentially the same thing, using one of the commandline tools, but it's perfectly possible to configure Calibre to always save this way right inside the gui.