I don’t know of any app that’s available for academic writing that is excellent on both iPad and Mac. If you’re intent on writing in Markdown then of course you don’t need to use one single app, although niceties from a dedicated Mac app may not be accessible.
If I were writing a dissertation that utilized references from something like Zotero/EndNote/Mendeley I’d consider a specialized Mac app like Manuscripts, whose workflow is similar to Scrivener on the Mac but is designed for academic writing. (Note: I have not used this app.) The main downside to it is that it is not cross-platform, and I’m not sure it works with iCloud.
https://www.manuscriptsapp.com/
Ulysses could be an alternative given your listed requirements, depending on how you’d intend to insert reference links. In this Reddit thread, the top-poster describes using Ulysses (along with LaTex, TexPad and Citations) for his/her thesis: