Eja ,
the motor tab are not supposed to fit in the slots of the decoder board , they are supposed to touch only .
However I still don't think Atlas have a nice design , it happened many times that after a DCC installation is done the lights works but the motor does not run . What I do is I solder a little lenght of wire to the brass motor tab or discard it and solder the wire to the brush caps . The wires have enough space to pass on each side of the decoder board and I then solder it on top of the board .
If you install the board upside down I don't think you will have clearance between components and the body on top .