No, the dev tool binaries are magic binaries that check if the "Command Line Tools" package is installed, and if not, asks you if you want to download it. They're protected by System Integrity Protection, so you have to temporarily boot with that disabled to remove or modify them.

I think it's a fairly common measure to download a lot of what OS X comes with over homebrew, simply because OS X's versions tend to be annoyingly outdated (Like bash 3.2.57, vs. 4.3.42 from homebrew).