FWIW, I think your son will be fine.
I am a homeschool parent, so I am the “principal” of my kids’ school so far as NMSC is concerned, and so I had to compete the entire “school profile” online for NMSC when my Class of 2015 daughter was in the NM process (yes, she got NM Scholar! Yay for her! Now I’m nervously anticipating the same process with Son #2, Class of 2017).
Anyway, a big part of the school profile is designating classes as the “most challenging available” (or some such language) for each content area in your school. . . I forget all the details, but it was something along the lines of Science, English, etc., and you COULD designate multiple classes for each category, so AP Chem and AP Bio could both be “most” in the Science Category . . . etc. I think the school might actually have to list every course the school has to offer! (I’m not sure, as in my case, all I listed was the courses my daughter had taken, since she’s my oldest and obviously I’m not offering classes my kids don’t take, lol.)
So, in a school WITH AP Chem, regular Chem won’t be “most challenging”, but if Chem Honors is the most advanced chem offered, then it is indeed “most” . . . likewise any other subject without AP classes available, then the Honors (or even regular) or whatever class will be the “most” challenging . . .
For instance, in my “school”, AP Chem and Honors Bio and Honors Physics were all “Most” challenging because they were the highest level I offered in my homeschool. For English, we had 2 AP English courses, so those two were “most”. For Spanish, we just went through Spanish 4, so Spanish 4 was “most” . . . For history, I only offered one AP, so just that one was “Most”. I hope that makes sense. It’s hard to recall the exact details, but I hope I have helped somewhat.
The school profile information is quite involved, and clearly they are using it to identify kids who chose to take challenging classes vs. those who skate through.
Additionally, the guidance counselor (me!) has to input each course the child has taken all 4 years (including SR year) . . . and designate each class as either a “most” challenging . . . or not. Obviously, you aren’t going to expect many “Most” courses in the first couple years of high school, but would expect at least a few in Jr and particularly SR year.
Essentially, for every class in the kid’s transcript, it is designated as either “most challenging” or not.
I don’t really know what their criteria is for NMF on this topic, but I’m guessing that so long as some reasonable amount of “most challenging” classes are taken by SR year, the kid is going to be just fine. In some schools, that may be a slate of APs, in others, honors classes, in others, simply English 12, lol.
I’m sure your son will be just fine so long as the other aspects of his application are solid (grades, etc.).