Handling figures is the thing Word sucks most at, and I still don't know a good way to work around it. All the other aspects of managing a thesis/dissertation are doable with Word though. Auto-generated TOCs that update, sections and chapters, etc. goobster is right about Word: you have to fight on its turf. The features are there, but not necessarily in the way or place you expect them to be, but they are for the most part there.
I've figured out how it "thinks", and can make anything inserted (images, spreadsheets, other objects, etc) pretty much play nice. And if I can't I can always build that one page in InDesign (or whatever) output it to PDF, and insert that one page into the final PDF file as a replacement, before I print it. But man... there is NO WAY anybody else could collaborate with me on what I do. It's a completely broken process that only works because I have cobbled it together from the bits and pieces of apps that actually work. Handling figures is the thing Word sucks most at, and I still don't know a good way to work around it.
The trick to Word is to imagine that there's a vengeful poltergeist named Clippy lurking in the code and every now and then you have to click on extraneous radio buttons and disclosure triangles to appease his hunger for GUI-fucking. As soon as you accept that it's possessed you can just sorta go with the flow. Granted, it's bombastically retarded that in the year 2017 we have to put up with this shit but hey - vengeful ghosts.
My tip: perhaps try making whatever it is you need in PowerPoint. I've found it's much easier to design with, it has a layer panel and I think that if you meddle around with the settings you can set the page size to letter and export to PDF. I actually designed a small app using PowerPoint using the Appear and Disappear animations for my work.