Personally speaking, I think it is good practice to include whatever support is needed directly on the 3D model, and in more general terms to design and model with the printing process in mind. It saves printing and cleaning time as well as material not to mention guesswork at the time of printing to get the correct support parameters.

Having said that I've been meaning to try Meshmixer to generate supports for organic models, I like the concept of the branching supports.