College admission officials do recognize that it can be a lot tougher to earn high grades in a rigorous prep school than it may be in your local public school (or in less selective private schools). The admission folks are very aware of the grading systems at all of the most well-known boarding schools (and even at many that aren’t so well known). So your transcript will be viewed in the context of your school norms, and you won’t be compared to applicants from less challenging high schools.
Top boarding schools typically have strong relationships with the most sought-after colleges, but they also typically have throngs of students aiming for the same short list of colleges. So, when it comes to admission to the hyper-competitive places, there are pros and cons to attending an elite prep school. But you definitely don’t have to worry that a drop in your GPA (as long as it’s not sinking like a stone 😉 ) will hurt you if you choose to enroll.