I can think of two reasons. First is cost for extra jacks and associated real estate on the chassis. There is also a downside in that the cable used to connect the transport section to the DAC section becomes a huge issue (check out threads here on digital cables).
The second reason is that an internal connection avoids the SPDIF conversion and associated clock recovery issues. With a direct on the board connection it's easy to keep separate clock and audio streams for reduced jitter (think I squared S).
The second reason is that an internal connection avoids the SPDIF conversion and associated clock recovery issues. With a direct on the board connection it's easy to keep separate clock and audio streams for reduced jitter (think I squared S).