Its all about copying from /mnt/diskX to /mnt/user (or user0) and vice versa (ie to/from a disk already assigned to the array to/from the user share system). That will corrupt the files.
That's fine. Specifying /mnt/user0 forces the files to go directly to the array instead of going to the cache drive if its enabled for the particular share.
unRaid has rules to deal with that. Generally, the version on the lowest numbered disk takes precedence, but it can certainly be confusing. If you only copy to /mnt/user, then this situation will never happen. The Fix Common Problems plugin when running extended tests does look for duplicated files.
0777 / 0666 and root:root are perfectly fine.
Both have identical results. Either way if you do use either the CLI or the utility, ensure you don't run them against your appdata share if you have docker containers. You may impact there ability to run. If in doubt, Fix Common Problems includes "Docker Safe New Permissions" in the Tools Tab.