This is how I understand it: Your AA average score is dependent on the number of total questions you answer correctly, not including the PAT. So, for example, out of 190 questions (100 Science, 50 RC, 40 QR), if you get 170 right, that might be a 23. If you get 140-150 right, that might be a 20 (the actual score is going to depend on which version of the test you're taking, and how others did compared to you).
This means that your Science score will count more toward your final AA than the other sections, based on the sheer number of questions in that section.
The TS (Total Science) score is calculated in the same way: how many questions you got right out of 100, compared to other people who took the test.
In other words, the score isn't an average of your other scores, but is calculated based on the number of problems you got right. This means that each question, whether it is from Science or RC or QR, is going to have equal weight toward your AA. This is also why a higher Biology score will contribute more to your TS score than G. Chem or O. Chem - there are simply more questions in the Biology section.