My son is also interested in engineering and baseball. He was recruited by 5 DIII schools, all of which had a 3-2 program, and were affiliated with an excellent engineering school in our area. Because of baseball, he wanted to stay on campus for 4 years. The school he chose had 1 senior who had been participating in the 3-2 engineering program. Both schools worked out a way for him to attend the engineering school in the fall of his senior year, but to enroll and take classes at the DIII in the spring, so that he could still participate in baseball.
My son chose a different route: he is going to major in physics, minor in math, and then get his masters in engineering. With the help of the college coach, he was able to talk with an admissions counselor at the engineering school to see if this was an acceptable option.
There are ways to accomplish both. If you son is interested in a school because of academics and athletics, have him discuss his options with the coach.