I agree, that comparing only spec-matched machines is only one aspect. Advertised prices that get people into stores (be they physical or online) are an important factor as well.A fair enough point, but even though we're locked into an Apple Monopoly for such upgrades, using Apple's retail prices to do so ... particularly when cross-shopping ... is problematic.
Is that a 3.1 GB/s SSD blade though?Case in point: your number shows that Apple is charging $300 for that +128GB SSD upsize, whereas the street (retail) price for a 128GB MBA blade is currently only $60, which means that there's a $240 "Apple Tax" on this feature normalization.
And a good deal of people will select to spend only $999 and either live with with 128 GB or probably more likely get a <$100 external (be it 3.5" for their desktop, 2.5" for mobile use, or USB stick/SD card expansion). Those customers are much less likely to spend a net $400 premium for a retina screen.As such, the alternative view is that this upgraded MBA should really only cost around $1060, not $1300, so the remaining differentiation feature (the retina screen) isn't really a $200 premium, but a $460 premium.
To some degree Apple has a problem here of only offering very premium storage that prices them out of some markets. Having a top-class display (not only retina but also gamut, brightness, viewing angle) adds to that (pre-retina MacBooks and MBAs had lower quality screen than the MBPs). Add cutting edge ports (the MBA got upgrades to TB2 two years after the MBP, getting TB3 on top of USB-C) is another slightly more premium classification.