Oof, yeah.
FWIW, I learned LaTeX for my honours thesis and that was a Bad Idea. I'm already an okay coder, so I was comfortable learning new languages, but tearing your hair out three weeks before submission because your thesis won't compile sucks. LaTeX (or even, to some extent, RMarkdown/Markdown) is for people who don't puke when they hear the question, "What if writing was more like programming?"
On the other side, I've written manuscripts in Word because that's what my colleagues were using, and sending references from Zotero was a bit of a struggle, especially with revisions (and that's before you bring extremely variable journal submission systems into it). I'd say learning to use a good reference manager is a pretty universally important skill in academia.
I think pure Markdown based on Pandoc is a good compromise in terms of readability and "getting straight into writing"—once it's set up—but I think there's a lot of room for tools that abstract the learning curve away specifically in academic contexts (thesis, papers, etc.).
Services like Overleaf and Authorea are also trying to solve that problem, but they have their own limits and often ongoing pricing. I think Authroea's a solid choice for papers, but it had some limits around thesis structure when I last tried it (though that might've changed). It does allow 1 private document at a time for free and has git integration underneath, which is pretty rad.
EDIT: it looks like Authorea is thinking about how to better accommodate a thesis, but they're not quite there yet (and they want you to publish each chapter as a separate article, which either means coughing up for a sub or being able to make your chapters public as you finish each one).