Am I at a disadvantage applying to CALS out of state?

My own guess is that there is a targeted in-state %, and it tracks the relative funding received from the state. This funding has declining over the years. When I attended it probably was 70%; maybe more. But in recent times it has been around 50%. When you see a percentage stay very nearly the same for a good number of years it can be speculated that this is not a complete coincidence.

And furthermore my guess is NYS residents do have a bit of an admissions advantage in applying to the contract colleges.
There are a number of reasons that NYS residents should prefer the contract colleges at a greater rate than applicants to the endowed colleges do: discounted tuition, unique programs that are not available at many other proximate colleges & universities. But I’m not sure these features completely bridge the gap from 48% in-state vs 20% in-state at the endowed colleges.
It’s possible that they do. My guess is not quite though.

But I may well be mistaken. Discounted tuition, for one thing, is a powerful feature. The “real” SUNY universities, with much lower tuition, have yet higher in-state enrollment percentages than Cornell’s contract colleges do.

However there is no completely on-point available data, so this is all just speculation.