The battery time estimates are based on certain usage patterns, not 100% utilization of power-hungry apps. A battery that can last "36 hours" can offer more real-world usage per day than one that only lasts for 24.
Edit: Looks like the only estimates Apple provides any more are video playback hours, which is much more power-efficient than general app usage and internet browsing.
Ultimately "all day"/"36 hours" are marketing labels that are at best rough approximations of reality. Your original argument sounds like "if Apple says that the iPhone Air's 3,149 mAh lasts all day, then a 4,500 mAh battery is useless", but as any heavy phone user can attest, with high usage even a new iPhone battery will need to be charged midday, regardless of what Apple says, and an extra 50% battery capacity can be the difference between regularly needing to charge midday and not.
Do you really think they couldn't?
The magsafe battery thing is actually pretty neat, but not using it to instead have a thinner phone feels pointless because you still have the giant bulge from the camera.
