I think the confusion is caused by mixing two things - abstract model of git repository where edges are just deltas between images of file system and implementa

I think the confusion is caused by mixing two things - abstract model of git repository where edges are just deltas between images of file system and implementation where this is all optimized. But you don't have to think about implementation when working with git, just abstract model should be enough most of the times. Sure, you have to think about particular implementation of git when for example getting rid of large files in repository