Note: "This rule only applies to courses typically at level II and III in a major (or in some cases level I courses considered to be core for the major). It does not apply to fundamental knowledge building level I courses in a major. Not all Bachelor of Science (Advanced) majors have advanced level courses, but where a major does, Advanced Science students must take these higher level courses. Please refer to the Advanced Science stream entries in this Handbook which indicate where higher courses must be taken."
So if we take the Chemistry major for example, the Chemistry courses are specified to be "Higher", but the other Level I courses allow you to decide whether you want to take the higher course or not. In Chemistry, the CHEM courses are considered core for the major, whereas PHYS and MATH aren't, hence why you can choose the lower options.
Which major are you considering?