I do use OneNote at work, but it's a classic example of where the tool molds the use case. Typically I will use OneNote to track a problem, or gather notes and links from other sources. It's a great way to put together a dossier on a problem so to speak, but I don't really use my creative juices in OneNote.
Also in time I found I never really used any version control features. Backing up to a remote was the only thing I needed.
I've resorted to using the original numbering system manually, but I'm still waiting for a tool that understands them and knows how to work with them (or maybe I'll get fed up after a while and make my own).
It's nice since it renders the markdown while you write it, which I kinda need when writing LaTeX.
It's an offline tool, but I'm pretty much always near my laptop, so that's not much of a big deal for me. Tbh, having it offline was kinda a bonus for me.
No Vim support though, which is a bit frustrating.
Next semester, I'm going to run the above command and then make a directory for each course I'm taking. In there, there will be a series of markdown documents numbered 'nn.md' with a header at the top of the file with the date and the subject. After that, it's just plain markdown. I alternate between VS Code and Vim, but both get the same job done. When I'm done, I just 'git add . && git commit' and move about my day.
Since I currently use GitHub private repos for hosting, if I'm walking to class, I can view the rendered Markdown right on my phone. This is nice for getting a quick recap about what the last class covered.
I also use a Git repo for my journal, but with different ways of formatting entries. The entire thing is very extensible, but not as friendly as some other note taking apps if you don't like plain Markdown. Writing a web interface for this setup wouldn't require much work, and it's something that's on my list of things to do.