One good reason to keep the raw data and orientation separate is hardware calibrations. I see some discussion here along the lines of "why not just flip the data before saving it", and one counter-argument is that you should store the flip metadata anyways, as it important to trace which hardware pixel corresponds to which stored pixel. I realize this information is not vital for everyone, but it is super useful in fields where you need to characterize the hardware performance at the pixel level (for example astronomy).