There's a decent open source sync daemon for OneDrive on Linux - I'm the packager who looks after it on Fedora. With the odd exception when APIs change it just works.
This does not appear to still be the case based on testing just now (creating a folder named ".foldername", containing a file named ".testfile" then verifying that they've synced up to OneDrive). Several years ago it didn't support syncing folders with a . in the name, but that was resolved 3 years ago.
With Microsoft's relatively new focus on Git, I can't imagine that problems with repositories stored in OneDrive folders would remain unfixed.
I will note that there are names that Windows Explorer won't let you create - notably, names beginning with a ".". That's an Explorer issue, not a OneDrive or filesystem issue - you can create such files and folders programmatically or from a command prompt.