A method of making a window unit is provided which may result in improved yields. In certain example embodiments, the method involves coating a substrate with both (i) a solar control/management coating, and (ii) a protective layer (e.g., of or including diamond-like carbon (DLC)) over the solar control/management coating. The protective layer protects the coated substrate from scratches and/or the like during processing prior to heat treatment. Then, during heat treatment, the protective layer(s) is burned off in part or in whole. Following heat treatment, the coated article (substrate with solar control/management coating thereon) is coupled to another substrate in order to form the window unit.