My biggest take-away is the saturation of advertisements and the effects it can have on running ad campaigns. Yours seem to focus on the common correlation-causation misinterpretation, and faulty measurement approaches.
I do think there are enough problems with the paper to not grant it the authority to speak for an entire industry (as Slate put it). eBay is just one (and a very big and unique) advertiser in this arena, and every move it makes (even to measure it) changes the entire ad network.
> They also used a geographic split as a control.
Thank you for this correction.
Aside: The problem with eBay's non-profitable advertisements seems to me a beautiful problem: The paper authors subscribe to the benefits of saved costs. I do not think that the marketing department of eBay subscribes to this benefit. For them, and external ad agencies, the more ads your run, the more clicks you get, the more you get rewarded, the better your monthly reports look. People at eBay's online marketing department must be smart enough to realize that many of these ads were worthless to the company, yet it was worth it for them to empty the monthly budget on a list of generic keywords.