Do you react the same way when an OS prevents you from writing to a file with an exclusive lock placed on it? So much for "a file is simply a collection of data stored as a single object"...

If a git repo was purely a collection of meaningless pointers and graph nodes, git would be a graph manipulation utility, not a version control system. The fact that some of those pointers have a meaning is what makes it useful and it doesn't contradict the fact that what you're working on is still just a bunch of pointers and nodes.