I have an external HDD with about 2TB of data, which I backup on another external HDD. This happens on a Windows and on a Linux PC, which obviously have different paths for the same files. And even using only Windows, the drive letter sometimes changes.
Even if no duplication happens, rescanning all the files takes 10+ hours.
That’s what I thought too, then I saw the paths for stored files where relative to snapshot metadata root? Now that I think about, that would be a problem with multiple roots. I will look into the issue you mentioned.