Actually, Flash for the Mac does not have an auto update mechanism. Many people rely on Apple to supply Flash updates by way of OS updates. It's been that way for years. The latest spate of security issues with Flash has changed the landscape a bit.
When Apple qualified a version of Flash to ship with an OS update, but that version is a revision behind what Adobe has publicly posted, Apple is given shit for not having the latest update in their distribution. When Apple decides to let Adobe do the legwork in getting the newest version into peoples' hands, Apple is given more shit.
I don't see this being much different from the position on Java: third-party crap that they don't want to be responsible for anymore.
If Adobe wants to have Flash be up to date on the Mac, they can do it themselves.
As an aside, but as a still peripherally-related statement, about the only third party software I'm in favor of Apple supplying themselves is printer drivers. That stuff is constantly changing, and though I rarely print, I think that it's more important to support those vendors and get the latest print software out there than to get the newest versions of slow, antiquated runtimes onto machines.