Installing a DCC adapter board is a waste of time and money -- just hard wire a 9-pin JST harness into the loco. I never use the Athearn "fire in the cab" bulb or clip -- I remove them and use a Golden Glow LED for the headlight.
Whenever I upgrade the lighting on my Athearns, I always remove the boards on them for two reasons.
1. The lighting outputs are 1.5 volts. I upgrade to LEDs which require about 3 volts.
2. Space. There isn't much room. In fact, yesterday I got an Athearn like you are explaining, but in the RTR line. I couldn't place the decoder on top of the motor because the board won't allow the body to fit on it properly.
Will