To answer this question, first answer the following question. "Does the MCAT award points for note-taking on the passage or for picking the best answer to a question out of four options?"
It doesn't hurt to keep a running list of definitions and equations you find useful, but note taking on the reading is typically not worth the time you invest. You are much better off taking notes on the questions. When you go through the reading part of passages, take a few study notes. When you go through the questions take thorough notes on what you needed to know. That will help greatly.
And most importantly, of all the reading you'll do, the answer explanations are the most important by a mile. Even when the answer explanation to a simple physics question is ten to twelve lines long, it usually has test taking tips and strategies that prove very helpful.