My (poorly-informed) opinion :
-One or more of these schools (the less selective) may give you a GPA break because it is a peer school,
-while the most selective of them won’t.
What schools are most worried about is that the transfer student will succeed at their school. At my alma mater the average transfer student’s GPA dropped 1/2 point after transferring. hence the concern. But a 3.45 at my school would be a perfectly fine GPA there. The fact that you acheived that at a peer school that is just as difficult should bolster the argument that you would succeed there.
Most of the transfer students are from “worse” schools. They did very well at them, but there is a question as to how that will translate which you won’t have.
So here’s poorly-informed data point #1: MY D transferred to one of these schools from a top-30 LAC and her GPA was not much different than yours.
But now to “bolster” my other point, here’s poorly-informed data point #2:
This one is from antiquity. At one point, following two dean’s list semesters at Cornell I toured Princeton, and had an informal chat about transfer admissions. The fellow said to the effect of, “well we turn down applicants from Cornell with 3.9 GPAs, so…”
FWIW, Cornell takes relatively a lot of transfer students. Also there are three different colleges at Cornell where you can undertake a biology major: agriculture, arts & Sciences, and “biology and society” at the College of Human Ecology. They each have separate admissions.
Whether Cornell will resolve your issues with Williams I can’t say.
Also, just because they give you a GPA break, so your application is not discarded for reason of GPA. does not necessarily mean they will admit you.
It’s still a crapshoot. IMO.