Your data is fully deduplicated, it doesn’t depend on the paths being the same as deduplication compares chunks of data.
Yes, restic will happily back up both your Linux and Windows systems into the same repository if you ask it to. And your data will be deduplicated (e.g. a file that’s more or less identical between the two systems will be deduplicated).
Your last comment is pretty moot - Restic is not what determines the paths you back up. If you back up different paths, for whatever reason, then they are different. If you back up equal paths, they are the same. It’s not something that restic affects. Hence, if your files should have the same folder structure on both systems, that’s something you must address on those systems, it has nothing to do with your backups and restic.
There is a nice PR from @aawsome that you are very welcome to try if you want to - it allows you to use a new
--set-path option to the
backup command to rewrite the path(s) you back up (e.g. back up
E:\foo\bar but make restic store that as
/foo/bar, which would then match the paths when you back up
/foo/bar on your Linux system).