Yes, you can. I have all of my students apply to both the SAs and ROTC. It creates a great Plan A - B - C for you.
"A" is one of the SAs, Plan "B" is one or several ROTC scholarships, and then "C" is the set of civilian universities that you apply to as part of the ROTC application process. I have had three students who won a scholarship or simply joined ROTC on campus (as part of Plan C) and then won an appointment (3 of 3) the following year. One of the students is graduating on June 1, USAFA C/O '23. Some 25 - 30% of all cadets at the SAs did not come directly out of high school as many attended a prep school, or a year or two of college, prior to becoming cadets.
Last year, one of my students turned down "plan A" and took a AFROTC Commander's Leadership Scholarship. It's great to have options!