It is over engineered, but not so different from some other tools. I think RawTherapee and others (such as NIK and its control spots) use them to avoid having to use layers and layer masks. If you know what you are doing you can make pretty good layer masks based on colour or tonality, and I find it easier to see and control the effects using a layer mask.
The problem with layers and layer masks is the amount of memory needed for each layer and its mask.
RawTherapee was never intended to be a full blown photo-editor so it is not surprising that it does not have brushes. If I want to do something that needs a brush I go into PhotoShop.