The typical over-achieving student is going to be in dozens of activities, none of which necessarily correlate with their future career. Agriculture might seem really weird or foreign to you, but for much of America being in FFA/4H/Eagle Scouts/whatever is just as normal as band, chess or sports.
My daughter is an officer in 4H - a horse club. I'm quite familiar with the organization. My point was that for those kids that fit the stereotype that the authors were picking on, high achievers with interests that don't fit the "elite" school stereotype, the admissions folks may have a point. The Harvards of the worlds may not be the best school for those kids. It's not necessarily evidence of bigotry.
They don't do biology at Harvard?
4H isn't specific to future farmers. (Heck, Future Farmers of America, aka, FFA, isn't specific to future farmers.)
If you're going to argue that a specific kind of discrimination is rational, shouldn't you actually know what you're talking about?
I think you are right, an agriculturally inclined student probably would not feel like they fit in at Yale. However, Cornell is also an Ivy, and they have a serious agricultural sciences program.
The article also mentions ROTC. I was once a TA at MIT, and there were many ROTC students at MIT. I believe MIT is now not just considered an elite engineering school, but just an "elite" school like the Ivies. And, I don't think they discriminate against ROTC students.
Furthermore, if they aren't already, the elite American universities of the future are Stanford and NYU, which seem to have much different student preferences than the Ivies or even hardcore engineering schools like MIT and Harvard, even though they are all lumped in together.
It factors in the opportunities a student has and admits students who therefore appear to have less going for them (it uses other metrics, a big one is being project oriented). It has at least in times past actively recruited white working class male students from the Midwest because they were underrepresented.
MIT has a big advantage, for there are no legacies to speak of. Everyone has to pass one year of the calculus (first term is the AP BC curriculum) and one year of calculus based physics. So MIT admits nobody who can't do the work. Legacies will get a "second look" if they don't make the first cut, but that's all. (As it is, the raw odds of admission are 1/3 if MIT thinks you can do the work.) It doesn't take many students from the fancy prep schools (I don't think many apply, MIT never was part of the elite prep school to Ivy/Ivy imitator path). So it simply has a lot more room for working class students.
Anecdotally, it doesn't seem to discriminate against Christians or students who have made achievements in those institutions cited in the study where for the normal elite colleges their chances of admission drop by 60-5%. As you note, MIT has ROTC units (if you get an ROTC scholarship at e.g. Harvard you have to go to MIT for the classes and other activities...).
(BTW, Harvard is not a "hardcore engineering school" ^_^. Although they did try to assimilate MIT in the years before it moved to Cambridge, that even led to a street riot in 1904 or 5. Heck, Harvard is so unhardcore that the last time I checked (end of the '80s) all you had to do WRT math was to prove you could do algebra.)