I’m using a Mac at work and a Windows machine at home, synced via Dropbox. This works beautifully.
I think there’s a discrepancy in how each is counting words, though, as there’s a 200 word difference. The Mac says 4000, the Win10 laptop says 4200. Both are upgraded to the latest version of Scrivener, and I haven’t played much with the settings. I’m not sure where I would change word count rules.
It’s probably something glaringly simple and I’m missing it. 
I’m having this same problem, only the difference is between 2K words instead of 200. x_x;;;
I’m at a loss as to figure out how many words exactly I have.
UPDATE: I’m compiling everything to a .docx and checking it in LibreOffice. Thus far, according to that, LibreOffice is closer to the Windows version wordcount than the Mac wordcount. I’ll have to play around with the settings when I get home (It’s a mac mini).
I recall having to do something similar in past NaNos, actually…
One thing to check out for aside from small algorithm differences is the compile settings. Mac and Windows use separate compile settings, and your Project Statistics word count is based on that. So if for instance the project is set on Windows to include “Chapter” prefixes and titles but isn’t including these in the Mac settings, that could be adding a fair number of words. Or if the Mac is set to compile only a section of the Draft rather than the whole thing, that’d be cutting your count a lot too.