at cornell the exact class rank is not reported in the dean's letter - rather a rough 'recommendation' level ranging from 'good' to 'outstanding' [yeah - somehow they pack 2 more adjectives in between those two]. the recommendation levels are determined by your grades in the first 2 years, and the 3rd year is averaged in with double weight. how you stood with your pre-clinical classmates is factored in with how you stood with your 3rd year classmates. so in a strict sense, you are lumped in with different populations.
this doesn't matter much - ones preclinical performance merits about 1 paragraph [a transcript is included at the end, reporting H or P], whereas the description of rotations is many pages long and quite extensive - and there is a section contributed by the md/phd program [i belive the director contributes it].
since mstp's are usually so competitive for residencies [like many previous years, this years match rate was 100% 1st choice] the class rank aspect is extremely small.