Layer based workflow in graphics software started out as a special feature and grew to be a standard in most applications today, even in freeware. The idea of working on layers really isn’t new, light tables and cell animation have been around for a long time, they’re a material for a different story, though. ;)
Lowering opacity and blending modes are a part of the layers functionality – while transparency/opacity is pretty self-explanatory, the blending modes are a special way, you can choose, the layer is displayed and how it interacts with the artwork placed below it. You can use transparency with blending modes together, for even more possible results.