[cantankerous]

shows central security systems aren't automatically foolproof

That was never contested by anybody. What the flame worm showed was that there needs to be stronger security around private key portions of signing certificates.

any sort of local control or anti-virus by that same central security system

Funny how that works. Anti-viral software is a central security system that uses similar distribution and signing techniques as the app store! Not to mention, anti-viral software doesn't protect you from zero-day exploits, unpatched software, and brand new malware that tends to be the thing that causes the most problem. Not to mention metamorphic and polymorphic malware, which is getting more and more common and runs circles around modern AV software.