After using Screenflow a lot, I have come to appreciate its capability to hide desktop icons. I miss this when I’m using Scrivener. I know I can use composition mode, but I find it too cut off from the rest of my Mac apps. I suppose I can fire up Screenflow and use it to hide the desktop icons for now.
I don’t know what Screenflow is all about, but why would Scrivener concern itself with desktop icons? Shouldn’t that be up to your Finder settings, or whatever other programs you use?
It’s rather out of scope for Scrivener, especially since, as you point out, it already has the distraction-free composition mode. There’s other software out there specifically for hiding (or better organising) items on you desktop, but you can turn off drawing the icons by firing up Terminal and giving it the following:
defaults write com.apple.finder CreateDesktop -bool false
killall Finder
Then just repeat but with “true” when you want to have them displayed again. If you’re toggling it frequently, you can use Automator to turn it into a service item available from the menu. I’ve attached an example workflow here; just unzip that and put it into your ~Library/Services directory (create one if you don’t have it) and you’ll get a “Hide Desktop Icons” menu entry in [ApplicationName] > Services, so you can easily turn this on and off while you’re working in Scrivener. If you’re really passionate about it/really want to procrastinate, you could tweak the automator workflow to automatically hide the icons when launching Scrivener and show them again when you quit.
Note: Because this prevents falling back to Finder when there’s no focussed window on the screen, you may get some seeming quirks depending on which version of OS X you’re using and what you do with Spaces/Expose/WhateverAllThatIsCalledNow. E.g. I run a VM on 10.8.5 that auto-hides the menu, so when I swipe from there to a desktop with no open windows, the menu bar stays hidden until I switch focus to a new app.
There’s also of course the other option of just not saving stuff to your Desktop… 
Hide Desktop Icons.workflow.zip (56.1 KB)
There’s also regular full screen mode as well as composition mode, which will cause Scrivener to take over the whole screen and hide the Dock…
Screenflow is a rather good application for creating Videos/Screencasts from your computer - which is an application where it does make sense to hide your Desktop icons so that your “PORNO OMG NAKED” folder doesn’t accidentally appear in the background of what is otherwise meant to be a professional presentation.
But outside this rather niche use of screen grabbing software, I agree that it isn’t a good idea for an application to play with the environment like this.