Why is the default mission setting for short runs across an elongated mission?

It doesn't default to the short runs. It defaults to North/South on iOS. You should certainly be using the rotate tool to suit your flight requirements and optimize flight time.

That being said, there actually are benefits to going the short way across the survey area (within reason). If you have a REALLY long survey area that takes 10 minutes to fly across then your images at one end of adjacent passes will be 20+ minutes apart in time. This is plenty of time for the shadows to move and change the features.