Alexander and his team absolutely expected people to adapt the patterns to individual preferences, and so stated right up front. As a matter of general preferences, “light on two sides” was found through diligent research to be a “deep and inescapable property of a well-formed environment”. So if you’re designing a habitation for thousands of people, maybe lean heavily that way.
e.g. Active college students, so also mostly young, mostly unmarried, freshly liberated from the parental household.. And of course the main activities of the building and its rooms, like sleep vs work, should be considered more strongly before applying a general pattern. I don't mean to assert that form should always follow function, though, or that architects don't already consider inescapable tradeoffs, which by their nature some people won't like the decisions because they would have traded differently all else equal.
On a tangent, I was reminded of a funny architecture crime. CS students at MIT got a wacky Gehry building (the Stata Center) while the architects have and keep a very normal and tasteful building (the Rogers Building). Gehry was even sued at some point because the building had functional issues. That goes back to the point about windows: frequently it's actually not enough to just block a window. They change the environment more than just letting in light or not, they affect things like temperature (sometimes for the better! Ability to open one for a breeze or window AC is a blessing in many rooms), humidity, structural soundness, and ease of mold growth. When you have a window or two in the bedroom that you block out, it still affects where you can place things because of those other concerns.
You rent a different apartment. I don't know what's so difficult about this concept with regard to his building and the need for some people to call it a hellscape. He's trying to offer a less expensive place for people to live for a couple years while they go to school.
A dorm room is not a habitat. It is just one room that someone will occupy for part of their day, mostly while asleep. He hasn't blocked out the sun.