No one here will be able to know for sure, as we do not know what is typically expected for kids aiming for highly selective”ivy-plus” type schools from your HS, nor do we know how many per year get into those schools from your HS.
Sonce you said some classmates were able to take AP phys1 last year and/or fit in an extra AP last year, then clearly it is done at your school(though 5 kids doing it versus the top 1/3rd will make it less significant that you didn’t). However, that was not the choice you made and that’s ok (or your teachers may not have encouraged that path if they did not think you were ready—that is the case at our kids’ HS, highest rigor is usually teacher/advisor-invited, and involves sacrificing a study hall).
You can certainly explain why you took the courses you did, just talk to your counselor about the best way to state it, or ask them to explain in their letter.
Bottom line: for the vast majority of schools, slight differences in rigor probably don’t matter much. For the most selective, it could matter, especially if lots in your school took a harder path. If there is no other way to get the extra AP you want for senior year, then you have to move on from what you cannot change and just put your best foot forward with the schedule you have and know there are many great schools out there.