I think this is a pretty disingenuous analysis of what's going on. It's obvious from the comparison to the [Virgin America] search that this is a bigger change that just adding a "banner ad".
Notice that for [Virgin America] there are _two_ spots that bring you to virginamerical.com, the ad and the first organic result. This is redundant, wastes space, and probably is confusing to some users. I don't know why a company buys ads for navigational queries where it's already the top result, but they do, and I'd argue it's bad for users.
On the [Southwest Airlines] query you can see that there's no redundant ad anymore - the navigational ad and the first organic result are combined. Calling that whole box and ad, when it contains the same content that the former top organic result used to, is misleading, but makes for a much more sensational headline when you want to claim that most of the screen is ads.
I'm not sure about the experiment, that's not my area, but my guess that this is part of an attempt to not have this ad+organic confusion for navigational queries by allowing the owner of the first result of a nav query to merge the ad with the result into a professional and official looking box. Maybe that'll work, maybe not, which is most likely why it's an experiment.