As you know, getting into a highly selective selective school is difficult. If you are defining selective as a top 10 university, then any of them could fill their class with students that have perfect SAT scores and a perfect GPA, but they don't. For example MIT only selects 50% of their applicants with perfect SAT scores. So, something in your application needs to stand out to make them want you. A ROTC scholarship could be that hook. It may not make any difference at all. But, you will never know unless you try. Duke has a NROTC program with single digit midshipman per year, so an NROTC scholarship may make a difference since they want to keep a viable program on their campus. Bottom line, I would make sure admissions knows you have a scholarship and I would make sure you contact the school's ROTC battalion to see if they can provide any support with admissions.
You also know there is a financial difference between a NROTC scholarship and an AFROTC type 2 scholarship. At selective schools with a cost of $50-60K per year, the type 2 will "only" cover $18K of tuition where NROTC will cover all of the tuition. For both room and board are not covered.
I would like to know more specifically about the federal microscope that
@pv123 references. The only specifics that I know of is the "tenuous" (not sure if that is the best descriptor) relationship that Brown has with ROTC programs, but nothing like a federal investigation.