Why does make world clobber my existing installed binaries?

Yes, this is the general idea; as its name might suggest, make world rebuilds every system binary from scratch, so you can be certain of having a clean and consistent environment at the end (which is why it takes so long).

If the environment variable DESTDIR is defined while running make world or make install, the newly-created binaries will be deposited in a directory tree identical to the installed one, rooted at ${DESTDIR}. Some random combination of shared libraries modifications and program rebuilds can cause this to fail in make world however.