I just changed the way I was using the borders with the latest version. I basically took the normal size of the border assets and trimmed them down to fit perfectly around the bag windows. This leaves a little inconsistencies in some of the information panels (ie. crafting window with a recipe selected) however it is hardly noticeable. Also, changing to the solid black (0% transparency) makes all the windows much more readable.
Overall, until we can trim down the actual window size via XML and remove those labels all together, there's no real way to avoid the nuisance of having to "activate" the bag window you want to negotiate on the three bags that have their bottom rows covered by the lower bag's label.