The procedure for the construction of boron-doped graphene nanoribbon using the "Builder" tool is correct. But the atomic structure of graphene nanoribbon is not same as the one shown in that APL paper. In that APL, i.e., Figure 1(a) therein, the two edges of nanoribbon are asymmetrical, while you constructed a graphene nanoribbon with symmetric edges. In addition, the width of graphene nanoribbon in your constructed model is also narrower than the one in that APL paper. These may be the main reasons why you didn't get the desired band structure.