This MacRumors thread says that someone's 64GB MBA came with just over 48GB (= 44.7 GiB).

http://forums.macrumors.com/showthread.php?t=1092617

I don't understand how the system uses different amounts of space on different MBAs.

I'd like to know this too. It seems one could not make a similar comparison of Surface Pro 64 GB vs. MacBook Air 64 GB.

Perhaps the MBA 64 GB has hibernate image file removed or some other similar tricks?

Metadata overhead is proportional to the size of the disk, as is flash reserve space. Also, Apple might have sensibly left some stuff out of the 64GB image.

Block sizes get bigger on bigger disks, so files that take up partial blocks take up more space on a bigger disk.

But that wouldn't account for almost 15GB difference between the 11" 64GB MBA int hat forum post, and the 13" 128GB MBA in the article.

It's terrible whatever it is. And it hates network drives. And iPhoto and iTunes hate remote libraries. And then they create local ones without asking and mess everything up. And if 2 computers share the library terrible things happen to the library and it gets corrupted (presumably the library stops matching the locally held file and its very easy to accident use the wrong remote library as after a disconnection a pop up asks which library you want to use. Pay careful attention at this point as a database rebuilt is the minimum pain one will experience with a miss click.). And the OS hates telling you what is taking up space so good luck freeing it up. Never again - although the 64 was accidentally ordered rather than the 128 and I assumed everything would be ok. It wasn't.