I'll take a stab at explaining ... if I get it wrong, am certain others will correct.
When you first make a backup, Moodle doesn't know your intent ... ie, what you plan to do with the backup. Restore to another Moodle server, restore to another course, restore to the same course, restore to Canvas, etc. ,etc.
So whatever you've selected to backup has to include those video files. Backup might be large.
In the restore (really import) process, you are selecting the option to restore to existing course, which should mean your intent is to add sections/new content to existing course. That course to which you are restoring has no similar/exactly alike links to the videos.
When Moodle sees a file that is in the backup and it can also locate the same file in the system, it should simply point to the file that already exist in the file system. Thus, one could have 10 courses with a video link and in all 10 courses that video link goes to the same video file - one file.
If one tries to manipulate a backup manually, one had better know what they are doing ... or results are as you have discovered.
** You might, however, consider a plugin ... Sharing Cart:
'spirit of sharing', Ken