I never liked this metric to evaluate universities, as "money" and "income" are not the only reason we pursue a higher education. If I have used this metric to evaluate for my own education journey, it is probably super high due to cheap and high quality undergraduate education offered to me at National Taiwan University, and graduate study all on scholarship/assistantship with stipend.
Anyway, seeing this publication from SF Chronicle is still interesting, as Caltech, Stanford, and Harvey Mudd are high up there in terms of return of investment. it is probably so much biased due to these schools are dominated by STEM majors, and therefore the metric mostly reflect on the major-based return on investment instead of actually schools. In other words, if we compare UC Berkeley's STEM majors, is it really not as good as Harvey Mudd?
I just visited Harvey Mudd with my high-school-senior during the admitted students tour. It is a very interesting school and indeed offers something quite special: low faculty-student ratio, solid training and high quality education, especially for engineering and CS majors. However the $90,000 tuition really doesn't justify it with comparable quality of faculty and students at Berkeley. Yes, Berkeley is a jungle that freshmen needs a lot of navigation, and campuses like Harvey Mudd offers a much more organized learning environment and paved paths to guarantee academic success. However isn't college the time to learn how to navigate chaos and variable paths? If the student and family really prefers a well-paved trajectory, I do think Harvey Mudd provides strong foundation with its core curriculum requirements to ensure every student learns the basic in current day STEM field. Engineering students are probably ready for hire right out of college, and has a lot of potential to be technically successful.
It is actually sad that an US student's college decision is mixed with family's ability to pay. Student debt continues to be a hot topic politically and economically. Top universities nowadays offers very little merit based financial aid package and mostly only grant need-based financial aid. While it sounds good that universities will match each family financial aid, the end result is still usually not affordable for middle class families. It is hard for me to understand why the university estimates that I can pay $70,000 per year per child given my income. And as a parent, I totally understand the emotion burden caused by not able to affording my child's dream college. I do miss Taiwan's college system that the tuition is usually not too much a burden for families, especially for public universities.
Therefore I can only tell my child and others in the same situation: It really does not matter which university you choose. It is all dependent on how you make your college learning solid so that you continue to move toward life goal. Everyone has different goals in life, and as long as you are having fun in the pursuit, college is just one stop. How much you bring with you for the rest of life journey is up to you.