Flash Player is a built in component of Internet Explorer on Windows 8 and higher. Everything comes through Windows Update.
Flash Player in Google Chrome is a built-in component of Chrome. Everything comes through Chrome.
Flash Player for Firefox and other NPAPI browsers is distributed via Adobe and can be downloaded at http://get.adobe.com/flashplayer. The settings that you're modifying in the control panel pertain to this specific Flash Player target.
Because Microsoft has their own distribution requirements (testing, etc) that need to be addressed before they can ship, we may occasionally beat them by a couple days when delivering an out-of-cycle security release. Typically the difference is pretty negligible, and the synchronization issues are just practical limitations and a desire to get the fix out to as many people as quickly as possible when we discover something bad in the wild. We get a little bit of a head start on Microsoft because it's our product, but they do a phenomenal job of getting the releases out in a timely manner.