I have some experience with an 11" MBA and a HHKB Pro 2.
I'd say it works just fine. Currently I use the keyboard with a MBP 15", which also works great. For me, the keyboard doesn't feel too elevated.
Furthermore, it's not necessary to disable the internal keyboard. Just attach some layers of thick tape to the bottom of the keyboard (barely noticeable), such that it won't hit the keyboard of the Mac. I've used this approach since I got my keyboard, and it's perfect. I can highly recommend 3M helicopter tape, which will also work as feet which stick better to the surface. I posted a photo a while ago, but I can't find the link (I think there's a thread here somewhere on the topic).