I think most of the reasons have been touched upon, but to sum up my thoughts:
(1) Williams requires the SAT/ACT, while some peers do not.
(2) Williams markets itself perhaps less aggressively than some of its peers, leading to a more self-selecting applicant pool. Williams typically has the highest or among the very highest yields of liberal arts schools, indicating that the students who apply are seriously considering Williams, rather than applying on a whim when they are more focused on alternative choices.
(3) Williams requires an essay specifically tailored to the school, which weeds out a number of un-serious applicants who, again, otherwise might apply on a whim via the common application.
(4) Rural location dissuades some applicants who might apply to Pomona, Amherst, Swarthmore.
(5) Largest student body among its closest peers, other than Middlebury.
(6) Has not aggressively marketed itself to international applicants the way some peers have, so does not receive hordes of applications from, in particular, East Asia.
Various of these traits are shared by some of Williams’ peers, but when you combine them all together, you end up with a slightly higher acceptance rate. Ultimately what matters is the caliber of student body admitted, and there, the top four (W/A/S/P) are virtually indistinguishable (some have higher SATs, some have higher class ranks, some have more diversity, some have better athletes/artists, but ultimately, we are talking about similar overall strength of student body) from one another, and as a group are stronger than any other LAC. So long as Williams’ student body is not suffering in comparison to A/S/P, I don’t think the school is going to worry about acceptance rates. If it was, it could just give, for example, a whole slew more of fee waivers, or more aggressively distribute marketing materials. But that would result in a lot of applicants who are less likely to ultimately choose Williams, so in the end, what’s the difference?
Regarding Forbes, Williams has twice been ranked number one overall by Forbes without any apparent impact on its applications pool. I don’t think that generally affects anything. Williams has also been ranked number one for 13 straight years by US News, again, without any demonstrable impact on the applicant pool. I believe Pomona has boomed in recent years because it is the only truly elite LAC (Harvey Mudd is engineering-focused, Reed is idiosyncratic, and CMC is just not as well-regarded as Pomona, although all could be considered elite in their own ways) west of Iowa/Minnesota and clearly the best in California, which has an enormous applicant pool of students who increasingly are being shut out of Stanford and Berkeley.