Keep in mind that your average repository doesn't only contain code that is compiled and executed (or interpreted), there is also documentation, static assets such as images (that may be processed), configuration, computed files (that may make sense to pre-compute once rather than compute on a hundred people's environments every build), and so forth.

Also, it doesn't only include the current file set - they include files that have been deleted, been split into modular files, been merged, been wholesale rewritten, put into a new hierarchy (some VCS systems handle this better than others).

(I work at Facebook, but not on the team looking into this stuff. I'm a happy user of their systems though. Keep in mind that the 1.3 million file repo is a synthetic test, not reality.)