First off, Title IX compliance has nothing to do with comparisons to other schools. Secondly, Weehawken is cherry picking around just one of the three points of Title IX compliance and he does not understand the one he is focusing on.
There are three points of Title IX compliance.
1. Showing that the number of female athletes is in proportion to overall female enrollment
2. Demonstrating a history of expanding opportunities for women
3. Proving that a school is meeting the athletic interests and abilities of its female students
So, let's look at the three points.
1. Showing that the number of female athletes is in proportion to overall female enrollment
According to the linked article, Penn State has a 5.9% difference between female athletes (41.2%) and female students on the Penn State University Park campus (47.1%). If you count the male practice players on women's teams, which is the way they are tallied for Title IX, the difference would be slightly less. Either way, that is well within the definition of "in proportion to." Proportional and equal are not synonymous. For example, as a Penn State fan, I could say that Carter Starocci's head is proportional to the rest of his body. That does not mean that I actually think that his head is of equal size as the rest of his body.
2. Demonstrating a history of expanding opportunities for women
Since my time at Penn State, I believe that they have added three new varsity sports. Women's Soccer (1994), Women's Ice Hockey (2012), & Men's Ice Hockey (2012). I have heard that the women's club soccer team filed a Title IX complaint in 1980 when PSU denied their request to become a varsity program. I do not know what the outcome of that complaint was, but I doubt that the Feds would let PSU wait that long if they were found to be in violation of Title IX. While Pegula paid for the new ice arena and endowed the men's program, the PSU Athletics is paying for the women's hockey program.
3. Proving that a school is meeting the athletic interests and abilities of its female students
I haven't a clue how one goes about proving or disproving this point.