Is there any way to uncheck the “Include in Compile” box for all the documents in a given folder instead of having to check/un-check each one at a time?
Thank you.
Hold down OPT!
… or ‘alt’ as we’ve known it since 2001. 
It’s basically “Option” on my late 2010 MacBook Air, and on my wife’s late 2011 MBP. “Alt” is only the secondary label, so I’ve always called it “OPT” … and so am quite likely to continue to do so. 
I’m sure the OP will work it out.
Mark
PS I’ve been a Mac owner/user since about 1991, so am also probably set in my ways as a result.
Ha! I’m a mere newbie. 1994…
Why on earth is this not done in the way it is with all other Mac apps, where there’s a square with a dash in it above the check-uncheck series and that toggles mass check and uncheck?
Probably because it should be quite rare that you would ever need to do that. The checkboxes are designed more for permanent assignments to things that aren’t really part of the output, like chapter notes.
Secondly, such a device as you describe would not allow for partial changes as discussed above (though I see it was not mentioned that one can select some items in the Outliner or compile Contents list and then Opt/Alt-click within the selection to have it constrained by that). Mass toggling everything in the entire draft folder strikes me as something hardly anyone would ever want to do. If you don’t want to compile anything, then why compile? 
Tried the dropdown, and it gave me the folder containing the story (this happened to be an individual folder with only three version of the story in it); when I selected it, I could then check the version I wanted. But I suppose this is why I don’t usually use Compile for putting an individual story or article into Word; I just copy-and-paste it and then fiddle with the font, size, margins, etc.
FWIW, I write primarily shorter works. I find the minor inconvenience of occasional tweaks to the Compile Contents pane much less annoying than having to spend time in Word.
I have Word because clients sometimes require it, but probably use it for less than an hour a year.