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Of course there is the varying absorbability of the test subjects.
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That is easily accounted for by selecting test subjects of similar aptitude. Not as hard as you think especially if you are selecting from a current college crowd.
There are texts that simply do not translate well to ebook, not because they are harder to read but referencing back and forth between pages is difficult and time consuming. Hard enough in deadtree. However, these are generally not novels. Being able to go back some pages to reread something is still the hardest thing I do on an ebook. With a book, you have location memory, but not so much with an ebook.
To make this study actually reasonably well done, the researchers could have saved a lot of effort by requesting subjects bring their OWN ereaders. Presumably, those persons would already be comfortable with their own devices. The idea that you would get different results depending on whether you have a Kindle, Nook Glo, old beat-up Sony or an Ipad is nominal unless the light source in the room is very poor. If you don't own an ereader, you aren't part of the study. It certainly would give better results than their current claims.