Sorry I haven't responded, I was having computer troubles. So... First, my son is doing Pre-Algebra this year. He will likely go into Algebra 1 before summer break. So no Maths will not be an issue for him. His struggle with formal curriculum was with writing (penmanship). In elementary school my son has not had to do a great deal of output because he was incapable of doing so. Because of his AS his doctors would not listen to me when I told them he had a vision issue. They simply told me it was his AS. After 6 years of Occupational Therapy which did help in some areas, just not writing, we were told that our son would never learn to write beyond a kindergarten level. At which point we insisted on a Vision Specialist. After 12 weeks of Vision Therapy he went from Kindergarten level writing to end of 5th grade writing and a diagnosis of AS and ADHD to just AS. Every ADHD behavior just melted away.
Why are we using Apologia? Because it works... it is a great springboard for him. Because it is young earth. Because it is "Christian" without the beating you over the head methods I've seen in other "Christian" science materials .Because it is conversational and gentle. Because we've gone through several science spines and he was forever saying, "Mom, I wish they didn't always assume millions of years." and other such statements. Because TED Talks only come out once a week and they aren't very systematic. But probably the biggest reason is that it is not an overload of writing requirements that I've seen in so many Jr. High/High School level science text.
But I am open to other science spine suggestions for tandem or additional resources or something that is young earth but more rigorous with input but not so with output. He has read extensively in science so I doubt that I will really find a college level input Jr. High level output curriculum.
I think the point about the Apologia is for him to see that a science route will most always assume the thousands of years. It will most always assume evolution. It will most always find ideas like Creation and young earth rather ridiculous. That does not need to be your family's belief, but if this is a hang up for him it should be addressed. As someone wanting STEM, that hang up could mean fulfilling career and happy college experience or really frustrated and not excited about further schooling.
Young Earth science at the college level does not really have much mainstream credibility. Young Earth even at the high school level does not have much credibility. Whether that should be the case or not isn't the point. To accelerate your son in science toward future college work or toward a career in the sciences, now is the time to really come to terms with the way society views science and how his personal beliefs work there in. It isn't going away and it does have a major impact on whether the career is going to be viable for him.
My brother has Aspergers. He really wanted to be self employed. He felt self employment was some kind of character builder and a pinnacle of being a prosperous person. He put so much stock in it. However, his Aspergers makes him socially phobic (that is just one of the ways it seems to have really manifested with him. I am not meaning all Aspies are socially phobic)...like hardcore socially phobic. Self employment is just not going to happen. If someone were to have addressed this issue when my brother was 13, he could have either been working on it to mitigate his personal situation or coming to terms with a different career path. Your son does not need to change his beliefs, but he might need someone to help him negotiate ways to either discuss them or not be emotionally beaten down from them not being recognized. As a person with a lack of social recognition, doing that now would be immensely helpful. Changing curriculum to a more mainstream, heavier content approach would go a long way in that direction. Even if you do not want to change, it might need to be addressed just so that he is not blind sighted later or ridiculed for his deeply held beliefs by the social views of an important community to him.