There is an aspect of the Gra that is less known than the learning Torah part. That is the emphasis of the "Seven Wisdoms." [As mentioned by Rav Baruch of Shkolav in his introduction to his translation of Euclid's Elements. {the Gra: "According to the lack of knowledge in any one of the Seven Wisdoms, one will lack knowledge of Torah a hundred fold. "}
So while Litvak yeshivot tend to follow the Gra in many important aspects, there is still this part that tends to be left out.
Why? One reason is that to gain any real expertise in any field there is the 10,000 hour rule. [Which almost equals four years of college in that field.]So to gain any real understanding of Torah, one requires at least a good four years in an advanced Litvak yeshiva.
So the lack of emphasis is not a problem, but rather a lack of awareness of this approach of the Gra--such that at least after the basic four years, one can start to begin his or her education in Mathematics and Physics.
