Sorry for the dumb question; but does Apple have absolute control over Apps on its platform; or is it possible to distribute App to iPhone users without store?
Mostly. It is possible to distribute applications to jailbroken phones without Apple's help, but that's a minority of phones. When a new version of iOS comes out, a new method of jailbreaking usually needs to be found.
Stock phones can only install apps from the app store, or apps signed for that specific device by a developer. Developer signing is also controlled by Apple, though.
Stock phones can only install apps from the app store, or apps signed for that specific device by a developer. Developer signing is also controlled by Apple, though.