Nothing leads to a higher clock speed, it is a decision the Hardware designer makes (in a certain range). Thus the SoC is a little faster, but needs more power, which doesn't matter on a device with a bigger battery; So it could be on the Plus, too.Correct, it's not fully like X architecture, but certain parts of the layout are different leading to higher clock speeds and overall better performance, though the difference is not very big at all. Both versions of the A7 are very powerful.
But I think what we're saying is - the iPad Air already shows lag at some points, and the iPhone 6+ is actually rendering a higher resolution image than the 9.7 inch iPad, and it has the extra overhead of then downscaling this image which the iPad didn't have to do.
Never saw an iPad Air lag under normal conditions
I guess they saw, that the benefits of using a lower density screen are higher than the disadvantage of downscaling. It shows the roadmap for future iPhones, too.