S/PDIF sounds more analog than AES/EBU

The reciever chip would be the same but the interface would be different from the input connector to the chip, and of course you are using different cables. Any or all of this could cause it to sound diferent. You may prefer the AES if you used a different cable. Isn't audio fun.

As far as I know the only difference in digital data transmission is jitter. Jitter manifests itself by creating side bands at very low level - very audible since not harmonically related to their root frequency. It can make impression of "lively" sound but I'm not certain how it changes imaging.

>>if both cables are in the system,they will affect one another-as they both will present a load to the transport and/or dac.<<

Totally untrue.

Each digital output has it's own drivers. Operating two at once doesn't degrade signal level or quality. You just don't want unused digital outputs active to reduce noise.

Furthermore, most components will only allow one digital output to be active at one time. In most cases, but not all, you must change the output setting to toggle between the two.