Illustrator offers many different ways to do the same thing, right? I guess at some point it just comes down to personal preference. When it comes to Pathfinder vs Shape Builder tool, why (other than personal preference) would someone use the Pathfinder tool? Are there things that the shape builder tool simply can't do?
Besides the things Scott mentions, there is also the possibility to make the Pathfinder's operations non-destructive by alt-clicking the respective icons. This will create an editable compound path of the combined shapes, allowing you to release that compound and re-obtain the original shapes. Or, better, to edit the original shapes and have the compound update with the logical operation you chose.