There are disadvantages to having a separate dac/transport. One is the obvious, in having to have a digital interconnect between the two, which itself is never perfect.
The other one that not many know of is there are two clocks, one in the transport and one in the dac, and they are not sync'd to each other.
In a stand alone CD player there is one clock that serves both transport and dac section so they are sync'd together.
This is why Cambridge in their original Reference 1 Transport/Dac pair, had an extra interconnect between dac and transport to slave the transport which didn't have a clock, to their dac.
Also why Tent Labs made a very expensive mod board you could buy to put in your dac to get the clock timing signal out to the transport with another interconnect that you had to take the clock out of so it was then it would be slaved to the dac.
The advantage to having separate transport and dac, is that you can change the dac when you want a change in sound, and you can have multiple sources/transports if your dac has multiple inputs. There is no sound advantage.
Cheers George