Got it. Unless you have a very good reason to move to markdown only … it seems like Scrivener is your perfect app.
All my written work is either for the web (course websites, other kinds of websites) or as PDFs. I don’t really need to worry/use MS Word. So I have a certain freedom relative to other academics in terms of format of text based work.
The beauty of markdown for me is I can do 2 things at the same time: one markdown file to create both web-ready content and PDF-ready content at the same time. That’s a huge time saver for me, and a huge reduction of writing friction. But based on what you’ve written you are not in the same situation.
Another huge benefit of Scrivener is the ability to collate research documents (research broadly speaking as a collection of PDF documents). I don’t need that feature built-in, but if it’s very useful for you then once again it’s a big reason to stay with Scrivener.
I don’t remember the compile feature vividly. I think I just figured out the best way to export (for me it was multimarkdown). Maybe it took me awhile the first time, but now several years later all I have to do is press a keyboard combo to export all my relevant documents in one go. But it’s likely true that setting up compile the first time (at least for certain formats) might be a PITA.