Use Word for windows (or mac). You're going to want people to comment on your document, no professors are going to edit a Latex or Scrivener document. Your thesis also has to go through a secretary or two. Do you think they'll know how to program Latex?
I don't know about LaTex, but Scrivener's not meant to be used like that.
You never offer up the Scrivener project to anybody else (unless it's a collaborator). It's a composing/organizing tool.
When you have something to send around, you tell Scrivener to export it as Word, or RTF, or plain text, or a PDF. You then send that piece around.
For example, I completed a very large project (300K words), exported it to Word for an editor (who made changes in that document using Word's Track Changes), exported it to PDF for other readers who weren't doing any editing, and continued to work on it in Scrivener.
I then looked at the Word document from the editor in one window while I did or didn't make changes in the Scrivener window. I'm not finished with that yet, but when I am, I'll simply export a new Word document for the editor and new PDFs for my other readers, while continuing to work in Scrivener.
Eventually I'll be working entirely in Word, but not until the end.
I recommended Scrivener and continue to push it to the OP as a compositional tool. Organizational changes are trivially easy, exporting chapters or any combination of sections (either for readers or for himself) is very easy, and so on.
Eventually the OP will leave the Scrivener environment for Word (or other environment) because the thesis will be close to completion and he'll no longer be thinking about major changes. Then he can turn his attention to his university's templates (if any), reference management, etc. etc.
I have to say I wish I'd been in the OP's position when I wrote my PhD thesis in 1971: yellow paper, index cards, and I typed the whole damn thing myself, all 330 pages of it, on an Olympia electric typewriter. My university required that there be no more than 2 white-out corrections per page.
Last week I scanned it into a PDF for a student who needed it, and put it in Dropbox for him. While doing it I remembered places where I'd wanted to do something different but was constrained by chapters, pagination, and all the rest, and had to leave it be (or retype many pages). Life is difficult when you're using a typewriter and want to make a change 50 pages back.
It's a lot easier now, which is good.
