I’m sorry about the situation with your counselor. Though it is his job to keep you advised what schools he feels are realistic choices for you, the bottom line is that he should not have intimidated you into not listing all of the schools for which you wanted to try for admissions.
Let me explain what could possibly be the situation here. For the very most selective schools, admissions is difficult even for the very top applicants, even with hooks. I’ve seen legacy, athletes, URMs not get accepted. I’ve seen the very top students with the top test scores rejected.
There are certain things that pretty much have to be in place for even that small chance of being accepted. On an academic basis, one has to be top 3 in the class at most schools, be taking the most difficult courses, have very high test scores, including SAT2s, have top recommendations fro the counselor and teachers. Certain phrases like “one of the top students I’ve ever had” or “ unusual intellectual curious it’s” that make it clear that the recommending teachers and GC think you are the best in school are nearly always necessary to gain admissions.
Your GC controls the school REC and it’s very clear he does not think you should be going to those top schools. His relationship with these schools, any sway he might have got future students is at stake here in terms of the recommendation given. So it can become a self fulfilling prophesy when GCs steer kids from certain schools. It ain’t gonna happen.
All of this is a lot more subtle than the way I’ve described things, but yes, the LORs are very important in the selective schools admissions.
I do not know if Cornell allows a student who takes a gap year to apply to other schools during that time. You need to check that if you are considering this option. But realize, that you may still have to funnel any apps through the GC’s office when you applying
Yes, you can apply to transfer. You certainly can apply to grad school at these top schools. Two of my kids are getting masters at Harvard and they were not good students in high school or college. There are all kinds of graduate and certificate programs at many select schools.