I have just started with Manuscripts. I am also looking for an app to help me write "big" documents. My documents also need to include citations links and figures and equations. I can fully appreciate where you stand and what you are trying to find. Been there, done that (many years ago).
Following on your posting, I downloaded an opened Mellel. Immediately, I have to say this ... Meh. What gives? When you want to play around with a word processor-like UI to write a PhD, why not just use Pages or Word or NeoOffice?
To be rather blunt then (as if the above was not), my immediate impression is that Mellel is just another WYSIWG GUI word processor like Word, only with its own UI configurations. When it comes to writing content in the most efficient way possible, at some point, the bells and whistles put in front of you with such tools will just get in your way. I have seen it happen all too well and far too often.
At this point in your writing career, with what you have before you, I strongly encourage you to change gears. Focus first and foremost to find tools that help you first put content down in the fastest way possible. Leave the document management to a later point. Learn to write ideas fast and well, then learn to "make your final document pretty".
In this regards, eve after a short test run, my surprising impression is, Manuscripts is going to do very well at "getting content down quickly while staying out of your way". It is going to offer a place to focus on content first, then layout next. The only other competitor that I can truly see of equal caliber is Ulysses.
As far as citation managers, I might also recommend a different approach. Find something first and foremost that you immediately grasp as a solid database for your citations. It should allow you to tag, filter, and sort cleanly.. It should be intuitive to handle and less about "bells and whistles". Then, find a way to make that citation manager work with your workflow to create your document. Bookends looks good. So does Papers. So does Mendeley (the tool I use). Perhaps so does EndNote for that matter. My point is, any one of these tools exports a database content and/or has a way to "link" citations to your "word processor".
Finally, as far as having a good tool for layout management AFTER you generate your content, nothing beats LaTeX. It is free. You may bulk trying to use it for whatever reason. But ... it is absolutely the best.
I might also throw your words back at you. You wish for a product where you can "entrust your work". I've been using LaTeX for over 30 years starting well before when WYSIWYG was even invented. I can likely open my old journal articles from back then (if I could ever find them), compile them, and viola ... be back in business (well, except for the EPS -> PDF conversion step of the figures). So ... do you really "trust" that you will be able to open your Mellel document in 30 years?
This is not to say that Manuscripts does not have some of the other problems that you mentioned. I've noted some of my own already elsewhere. This is to say, your lament that Manuscripts won't do what you need is misplaced. I think you don't yet know what you really need. Also, your outcry that Manuscripts is an app that we might not be able to entrust with our work shows a bit more the extent of what you possibly do not know about how to evaluate this criteria properly in the first place.