I don't understand why would anybody imagine there's any difference. The things that actually matter are things that tip the balance in either calorie or nutrient counts, such as high-protein foods - protein BARS are a joke, those are pretty much chocolate bars with an obligatory small dose of protein thrown in and, apparently, used to replace 50% of the taste of an actual chocolate bar, while keeping roughly the same amount of sugar.
The study also used protein powder, which I feel is taken more seriously than protein bars.
Also, many of these products market themselves as having special formulas that are more efficient at getting energy to your muscles. Misconceptions about these things are spread by the people selling them, and they always make it look very legitimate and scientific.
I went to a DuPont field trip type thing and they showed the whole process of making stuff like protein bars, they actualy have a lot of protein for a granola bar because they put a bunch of soy protein powder/granuels/etc.. was interesting to see.
They also explained why protein drinks and some soy drinks can have a grainy texture
I've bought a protein bar yesterday, out of curiosity, as my parents mentioned they are pretty good, actually, and checked the nutrition data. IIRC it had 9 gram of protein and 23 grams of sugar per a 50g bar. That is mostly sugar and a token amount of protein (especially since I can buy a tasty mango yoghurt with less of the former and more of the latter for less).
Plus, protein supplementation can be really goddamn dangerous - if protein makes up too much of your energy intake, you tax your liver and kidneys which are normally processing those, with the potential for failure, especially for kidneys, as liver regenerates.