Because the data sources are unrelated. The camera sensor is hooked up to the ISP which is hooked up to a hardware JPEG encoder. This is necessary in order to get those hyper fast shots off.

You'll notice that an orientation sensor is no where in that list. So what happens is the camera hardware spits out a JPEG. The app then combines it with the orientation sensor & produces the EXIF headers. It could choose to decode, rotate, re-encode, but that's slow (~100ms) and hurts shot-to-shot latency. And it loses quality. And, hey, since everything supports EXIF orientation anyway, why bother?