> If you have rewrote a file 999 times, there is 999 times copy of this file in the object storage. That's why it can be slow to clone a git repository.

Sort of. While Git’s canonical storage is indeed not diffs, it uses delta compression to, well, store diffs as a storage and transit optimization https://git-scm.com/book/en/v2/Git-Internals-Packfiles