You are correct, I have write3 installed on my phone and need to use it on the desktop too for that same reason.
I keep having dreams of making a linuxnote for OneNote files since the file format is technically open specs, but as they are super complex and I've barely opened a hex editor before I just don't know what I'm doing enough to actually try parsing the bytes of an arbitrary file yet.
In the meantime, I'm using stylyslab write [0] which uses svgz and is a good replacement for OneNote and a compromise I'm willing to make to not be locked in but tbh the OneNote app is just so much better.
[0] http://styluslabs.com/