"why do application developers seem to think that it's alright to build their own outer frames for windows and ignore the operating system's configuration?"
Seconded. Like the Windows Media Player from (I think) Windows 95. Fancy looking window frame, but then the rectangular frame came back when you need the menus, and looked terrible.
Also, on Mac Yosemite the functionality of the green button only does 'full screen' (i.e. no menu bar). What's supposed to happen is if you hold ALT while you click it, the functionality changes to 'expand to fit content' like old pre-Mavericks OS X.