My DS is a college reapplicant in the NROTC program this year as a 4/C. Though I don't pretend to have any inside knowledge, the only difference he was made aware of is the way the college first semester grading and class schedule was weighted in the application process. Colleges in general and USNA in particular want to select candidates that will be successful. SAT, GPA, and class rank numbers are used by schools as a proxy measurement for likelihood to succeed at the undergraduate level. In addition USNA looks at the whole person with extra-curriculars, DODMERB and CFA being very important factors.
However, now that the college re-applicant has had a chance to attend a semester of college, the academy no longer needs to use a proxy measurement. They can use actual results. This re-applicant has had a semester to live on their own (wild card), experience the rigor of a plebe-like class load (assuming they take a similar schedule), and in the case of NROTC, show military aptitude(or not). This is direct and measurable data rather than an indirect proxy, so is weighted much higher than success in high school.
I'm on the outside trying to decode the process, so take all of that with a large grain of salt.