We have not gone through this process with regard to a child, but I do have some experience with early college.
1. To my knowledge, few colleges will restrict any of his opportunities as a 16 year old, outside of the obvious drinking age and legal contract restrictions. Dorms are usually insured down to 16 year-olds. Based on my first-hand experiences, there were (at the time) no restrictions on labs, overnight trips for field experiences (even across national lines), or student activities.
These would be questions to ask an admissions adviser, probably early on, so that it's not part of the admissions process per se, as you don't want it to affect his admissions prospects.
2. Transfer is not an unreasonable approach, especially depending on his interests with regard to academics and the college experience, and on your family needs. Many 4 year state unis take grads of approved state 2-year college degree programs in with all or nearly all credits transferring (and, in some states, at the CC tuition rate). You graduate with two degrees: an associate's from the CC, and a bachelor's from the 4-year uni, with no asterisk indicating that the first two years occurred on the CC campus.
3. If I recall correctly from previous threads, you may actually find it more challenging to arrange a gap year program that accepts 16 year olds than a college program that does.
