If and when I get hold of SM:P, I will probably do a reorganization of skills to reflect the specialization in modern, not to mention even more advanced, sciences. I agree that if you pretend "Chemistry" is a single skill, then "Math" might as well be, too. Although I suspect chemistry is a science that may be complete some day, whereas mathematics is certainly open-ended. If you're going space opera instead of realistic, however, you are better off ignoring specializations.
I had kind of assumed the new Spacemaster would have had categories like Science*Physics, Science*Biology, etc. with a Science "group", allowing a three-level hierarchy (with only Talent and Professional bonuses crossing the highest level of "Science"). This seems the minimum to reflect the structure of scientific knowledge and work with some accuracy.