I thought you were asking about whether Moteino MEGA without transceiver is == Arduino MEGA2560. Again, they are different MCUs so I belive to that question the answer is no. You can't use a MoteinoMEGA as if it was an Arduino MEGA2560, vastly different boards.
But to your new Q: If there is no transceiver installed, then yes, all the pins are free for other uses.