My post above was descriptive rather than explanatory; you can make the same observations yourself toggling the various functionalities (CtF, JavaScript etc.) on or off, but the effects may vary depending on OS/-version and browser/-version. That said, Autoplay is (a.o.) a Flash setting*, and as such secondary to allowing Flash to load. Via the plugin, CtF affects Flash loading directly, and Autoplay indirectly: you first have to allow Flash before anything can use that to Autoplay. That said, CtF can be circumvented with Javascript, ‘baring’ an Autoplay setting if present; depending on the website’s Javascript controls (and in part on the browser/settings) your Flash object Autoplays. Example: when I ran Safari 5.x under Mac OS X 10.5.8 (PPC) CtF effectively killed Flash, even on Autoplaying sites like Macworld. That no longer works with Safari 8/9 under Mac OS X 10.10.x, unless I kill JavaScript too.
*) an option which can be toggled in CtF’s settings on the Media Player tab
