[tldr; it's not permissions, but apparently yW hates network drives. Explanation, and possible separate bug below.]
*Snap of fingers!* You may be on to something, Boy Wonder.
I thought of that before, but I ignored the thought, because why would the permissions on Linux AND on Windows be the same?
...
Well, it's not that, but in testing it, I did discover something... and maybe I missed this somewhere, especially since it was working. It appears that yWriter hates network drives.. ? My My Documents folder is mapped to a network drive (it's a NAS that's local). I was able to set up and work with the project, but for whatever reason, this issue developed-- and it appeared to be once I set the project up on Mega, opened it on my laptop, saved it, left the project open, then opened it on the desktop and got this error. (It had been saved on the laptop, and once I realized it was still open, I closed it).
So, now, if I create a new project, and locate it on any of the network volumes on my NAS, I get this error. If I create a new project on a local disk, I do not. Similarly/oddly, I have a local folder that ALSO has a mapped drive letter via the loopback interface. I can create and re-open a project in there, using either method.
I ssh'd onto the NAS to check the permissions, and everything was the same as ever (fully open everything for my user account), and I checked on Windows, out of curiosity, and nothing weird there.
But, in case you missed it, if I create that .lock file it can't open, and then I close the aborted-opening project, it will erase the .lock file. So, it erases it, well enough. Also, I can write a new project to the same location.
Ultimately, my solution is a mess:
Copy my Writing folder to a local folder.
Sync local folder with Mega.
Backup/rename Writing file on network.
Create standard shortcut on network to point to local folder (in case of any existing links, etc.)
NOW, yWriter opens the file without any question, and even with all my monkeying around trying to fix the issue, it looks like it's all intact, so well-done-you!
I did just discover something, though-- I opened my project, the last scene I was working on is visible there in the Scenes/Content tab. But if I close the project, that scene remains there. Expected behavior? In this state, yWriter does not believe a project is open, as there is no Close Project option available.