For some reason, today, out of the blue, my project statics stopped working. Alarming, as I have 46,000 + words, and the project statistics, no matter how I compiled them, said I have 380!! I posted a frantic request for help, and then, two minutes ago, figured it out-- I had recently compiled the project in “outline view” and for some reason the project statistics remembered that view as my project settings. I recompiled in another view (standard novel) and it came back to normal. Somebody should probably look into this. No? 
That’s how it is designed to work. 
Granted, in the case of using the outline preset for compiling, that’s probably not the most useful result, but for most “normal” uses of the various compiler functions, you would want what you’ve set up as the document to be, reflected in the statistics. Basic common example: you write magazine articles and have five or six of them in your Draft as sub-folders. You are working on the fourth article in the series, so you’ve got it selected as the Compile Group in the binder. You don’t want to see statistics for every single article in the series—just the one that you are currently focussing on. So that is why this feature works the way it does. Granted, that’s not what you might always want—so there will be some extra options coming along in time, such as one that will always use the entire Draft rather than just the currently selected Compile Group. Any novelist that routinely compiles out single chapters to proofers will appreciate that option.
Even with that though, bizarre compile settings like the outline preset will still impact how things work, so just make it habit to set things back to something more typical when you’re done. Again, consider a common example where one types chapter notes into the folder that contains the chapter scenes. The folder’s Formatting settings would be set to exclude text output, only the chapter title. You wouldn’t want the text notes to be included in the statistics.
That will be made easier in the future, too. I don’t think it is coded yet, but a way of changing your compile settings without actually compiling should be in the works.
Ah, I see. Well, thanks for clarifying. This makes sense, although because there are settings in the project statistics dialogue that say things like “include everything” or “don’t include annotations”, it gives the impression that those settings will determine what you see in project statistics. It might help newbies like myself to have a little reminder in that dialogue that says “project settings always reflect most recent compile settings” or something like that. Those distinctions are well delineated as it relates to formatting in document vs. compiled draft… 
Yeah, I agree with you, this dialogue is a little confusing right now. The problem is is all of those options actually only pertain to the Selection, not the Draft. Eventually there will be some Draft options to, as mentioned, and once those are in it will be more obvious that there are two sections of options rather than just one that only impacts counting the binder selection.