Are you ssuing one of the files is just a link, like an alias?
I am saying, files of the same name, some size could be hard links. I don't know about Final Cut Pro X, because I never looked, but the original files in Photos are hard links to the original files in Aperture or iPhoto, but look perfectly identical:
The same original master file in the migrated Photos Library as in the original iPhoto Library:

You can tell that it is a hard link from the identical inode number in the Terminal using the "ls -i" command:
Last login: Sat May 23 07:46:46 on ttys000
Hermione:~ dreschle$ ls -i ~/Pictures/Aperture\ Library2015.migratedaplibrary/Masters/2015/05/23/20150523-185458/IMG_0107.jpg
37677881 ~/Pictures/Aperture Library2015.migratedaplibrary/Masters/2015/05/23/20150523-185458/IMG_0107.jpg
Hermione:~ dreschle$ ls -i ~/Pictures/Photos\ Library2015.photoslibrary/Masters/2015/05/23/20150523-185458/IMG_0107.jpg
37677881 ~/Pictures/Photos Library2015.photoslibrary/Masters/2015/05/23/20150523-185458/IMG_0107.jpg
Hermione:~ dreschle$