I agree that not all institutions teach the same, but that is the subjective nature of education. Using a single exam (MCAT) to standardize this sort of subjectivity is a touchy discussion that I won't get into.
If one wishes to take advanced courses prior to taking the MCAT, they can certainly do so with proper planning.
While I don't have any exact figures on hand, there are many non-traditional students who take those classes (and no "advanced" level sciences) and do well on the MCAT. As to "teaching to accommodate physics, bio, and chem in general" is precisely the reason why they are called General Physics, General Biology, and General Chemistry. The nationalized licensing exams med students and physicians take are a bit different in character (i.e., more knowledge-based) as compared to the MCAT; of course, good test-taking ability cannot be undervalued here.
Schools don't plan out a curriculum? That's a bit extreme. Syllabi are commonplace in the university setting. What you are describing above, albeit anecdotally, is a matter of how a professor chooses to conduct his/her course. It is true that there are professors that cannot teach effectively, so perhaps schools should be more rigorous in terms of finding the right people.
Maybe you should become an educator and revamp the system, then.
You're going to be faced with a lot of subjects in medical school that interest you as much as the worm phylums that you cite, so it would behoove an admissions committee to see that you can do well in those subjects that do not necessarily appeal to you.