There was a big stink a few years back when many of the elite Day and Prep schools announced they were dropping the AP curriculum. Doesn’t seem to have hurt them in the college admissions department!
I think your point is well taken-- but I think adcom’s are looking for evidence that a kid with solid grades and scores has challenged himself/herself. So not a kid “phoning it in” or gunning for an easy A. If in the context of your own HS that means taking the AP version of Bio for a kid who loves bio… then the AP makes sense. If your HS has a great science curriculum and a challenging Bio class which is just called “College Prep”, then presumably your guidance counselor knows how to explain that to adcom’s.
Where did kids like your son end up in the past few years? That’s going to be a great datapoint for you…