Alright was able to figure it out! The big issue for me was that I was using different durations in the gsap.to function which was causing all sorts of weird issues - I assumed the duration was the duration of scrolling time but it looks like it changes the scroll position value so it must work differently - not sure why but setting it to 1 does the trick.
$('.nav-link').click(function() {
var st = timeline.scrollTrigger;
var pos = st.start + (st.end - st.start) * (timeline.labels['section'] / timeline.duration());
gsap.to(window, {scrollTo: pos, duration: 1});
});
