Had the same issue with variant location inventory only reflecting the first location in liquid data when we have 3 locations. Our first location is enabled for store pickup but our other locations are not. Somehow, enabling store pickup for the other location impacted the liquid data so it now reflects correctly, almost like it forced a fresh cycle through the data. You can go ahead and disable store pickup after that if you need to like we did and it will still reflect correctly.
For reference, our store is Shopify 1.0. I’m curious if anybody is on a 2.0 store and experiencing the same issue?