Thing to remember is that if you want to apply for Melbourne's MD, you need to satisfy
second year (level 2) prerequisites, which are (well the recommended ones);
PHYS20008 - Human Physiology
ANAT20006 - Principles of Human Structure
BCMB20002 - Biochemistry and Molecular Biology
The prerequisites for these are satisfied by completing Chemistry 1/2 and both semesters of Biology in first year. So that's four subjects right there. Not all majors will include all three of these subjects in their pathways, so make sure you keep this in mind. Ecology and Evolutionary Biology for example doesn't have these subjects in it's pathway, but when you do a major, not every single subject slot will be taken up by subjects relating to that major, therefore you have slots where you can complete the MD prerequisite subjects. Therefore the Ecology and Evolutionary Biology major can still lead to MD.
If you look at most (if not all) those majors you listed, you will most likely need to do chemistry and/or biology in first year for most of them (in order to eventually satisfy the third year prerequisite subjects). I personally didn't decide my major until after my first year. Second year is the year where you have to start narrowing them down, and start choosing subjects more specific to a major.
When you're looking at subjects, the format of the subject code, i.e. PHYS
20008, the number right after the letters (that indicate department) is the level of the subject. 1 is level 1, 2 is level 2 and 3 is level 3 (there are other numbers for postgrad subjects and such).
With your medicinal chemistry major question, what you said is right, to have that major you need to do all four subjects, and that those subjects have prerequisites that have to be met. Taking a quick look at it, to complete all four subjects you showed there (all which are level 3), there are four subjects in second year (level 2) that you have to complete. Those four subjects in second year have chemistry and biology as prerequisite level 1 (first year subjects). However as I mentioned above, doing chemistry/biology in first year, doesn't suddenly limit you to only that major, because pretty much any major in that list you provided has chemistry/biology as first year prerequisites. It's once you get to second year where you begin to need to narrow down majors.
In all three years, provided you do what I mentioned above for that major, you have two free slots every semester, 4-6 will be taken up by breadth, and the other 6-8 can be science subjects you find interesting, that don't necessarily focus on your major (and to also complete the MD prerequisites), but ensure you meet the prerequisites for these too.
EDIT: Should mention that you don't have to do level 1 subjects in first year, level 2 in second year etc. however you have to make sure you keep within the credit points
limits you mentioned in your OP.