I know you were sent here from the issue on Github. I went there to get the link so I could send you there. Sorry if that is frustrating. 
There isn’t really anything to be done here either. Obsidian also can’t control iCloud. (As far as I understand, I’m surprised it can actually detect and warn you that iCloud is syncing.)
I assume your assumption is correct, and you’re experiencing an unavoidable race condition. It would be up to iCloud to detect that, and either duplicate the file, or do some kind of merge operation. (I have no idea how iCloud handles that. Clearly not well.)
Hopefully someone has a suggestion in terms of help. But I do know WhiteNoise often rejects bugs that are based around community plugins.
If you aren’t aware, for #4, you should hopefully be able to restore your old content with the “File recovery” core plugin on your Mac. Hopefully it grabbed a snapshot. Although hopefully you also have a backup you can restore. Please don’t rely on iCloud as a full backup solution! (imo)