You know the upside - here are the potential downsides to look into and consider (based on what I've heard from participants in another state's program that is similar to what you described).

1. It's a boarding school program unless you live locally. You are sending off your 16 year-old and losing a lot of your influence over him. College professors, many of whom will be leftists and who knows what else, will start having a major influence on him two years earlier than otherwise. You won't be able to provide much supervision to him if he's living 100 miles away. At 16, he's going to be away from home for the next two years under the supervision of people who may not share your values. It's your child - you know better than anyone else how he would respond to that type of environment.

2. His schools peers are not going to be very diverse - they're generally going to be nerds. I'm not saying this disparagingly (I'm an engineer), but he isn't going to have the same social experiences with a wide-range of people as someone who is going to a regular high school. His social development at school will be different than for a normal high school student. Might not hurt him in college, particularly at one of the top-tier engineering schools, but how will it affect him in the real world? Again, it is going to depend on the individual kid.

3. He probably isn't going to have the same high school sports and course options as most high school students do. Even if the special school has sports teams, they probably aren't going to be competitive with the schools they play and probably not very important in the school's overall mission (might be just another extracurricular activity). He probably won't be able to take high school shop/agri/industrial arts classes or home economics (family and consumer sciences) classes if he is interested in those. A lot of students aren't interested in those types of classes anyway, and he may have already taken as many of those classes as he would want to (and he could take them next year before he entered the program if he wanted), but that's just another area in which his high school experience would be different. I personally enjoyed those type courses and learned some real-life skills in them. I think this third point is probably less of an issue than the other two because high school sports aren't the be-all/end-all in life and he could gain the knowledge from shop/agri/home ec classes in other ways. The first two points are the most important IMHO.

As you know, you just have to weigh the pros and the cons. It could be a springboard to help him meet his life goals, but to a large extent, he would be skipping the last two years of high school and going to college (or perhaps more accurately a hybrid high school/college that is much more like college than high school). The cons may be relatively insignificant for your son, but those are some things to consider.