The loader has to be exactly where it is or it won't line up with the belt. Also, the loaders exist for one purpose only: to load belts into beltboxes. It never mattered to me whether they line up perfectly with any other entity.
Originally the loaders were designed to line up perfectly with the beltboxes. This was in Factorio 0.16 when belts were still flat. In 0.17 they changed the design of belts so that they are "fat", with height. (They also changed the design of chests around the same time.) I was able to tweak the loaders so that they worked with the new belts and were still almost in line with the beltboxes. There is about one pixel of tolerance for moving the geometry of the loader around and you have to deal with all the distorted geometry of Factorio's isometric perspective on top of a flat square grid. I spent about 48 hours trying to make it work in all situations and failed, so in the end, how they look with belts and beltboxes took top priority.
Anyone is free to redesign the sprites and submit a change to the Github.