Actually, Jerry Ozment, the late digital designer, told me that most designers who have multiple digital inputs on their DACs will have optimized their design for one of those inputs, so while mattmiller may be correct as a general matter, it can depend on the designer as well.
Toslink can be all right, but can be beaten by the other connectors if they are done properly. There's also the ATT glass output, which is generally regarded as a much better fiber optic link than Toslink. Also there's a bnc type of output which I believe is well-regarded--my old Forsell transport had that.
Widespreadpanic, as for your question on a transport vs. a CD player, the answer is generally yes in theory, as the designer can optimize the design for a transport and put the money into that design rather than having to also deal with the digital to analog circuitry and power supplies in the confines of the single box. But there are a lot of CD players that work well as transports, and the advantage to that is that you can bypass the digital to analog circuitry in the player to get a better-performing DAC when you get the upgrade itch.