This iPhone app should be able to control all windows up and down
I agree. In the past, the keyfob could lock the car and raise all windows. No longer. I suspect a small dog may have been choked or even decapitated

or ???
It doesn't make a lot of sense to be able to lock the car from a phone or keyfob when a window is open.
The windows do shut down for obstructions, but still...
It would also be nice if the windows and roof closed when the rain sensor (what rain sensor?) detected rain. If I'm not mistaken, the 1960 Cadillac convertible had this feature...and it would raise the top.