Interesting comment on that article by Siddharth Agarwal:
"(I work on source control at Facebook.)
Every problem you mentioned with monolithic repositories is a well-known problem with Git (though some of them do have workarounds, such as clone with --depth). None of them are issues in principle.
With Mercurial we're aiming to provide tooling that scales well while still maintaining DVCS workflows like local commits."