Are my junior classes good enough for Norte Dame and Boston College?

am currently taking or will take
APUSH 1.5
AP ENG Lang 1.25
AP Calc AB 1.25
Gym .5
Health .5
Honors Chem 1
Usually at my school people have 7 credits built into their schedule but because I decided to have independent study (A non credit class and will not show up on my transcript) I will have 6 credits. Will colleges punish me for taking the independent study instead of a class. I have mid 90’s for the 3 AP classes I’m taking this semester. My school does semesters with 4 blocks/ classes in each. So for the whole year I have 1st block as an independent study as I sacrificed my lunch and a .5 elective both semesters.

Here is what Notre Dame suggests:

https://admissions.nd.edu/apply/evaluation-criteria/

Whether that hurts you is dependent, in part, on the strength of the rest of your application. But the independent study, assuming there is validity in the topic studied, will not hurt you.