Yes, the rationale is that the audio signal is transferred in a digital chain only, e.g. from your sound player to the operating system's sound system, the sound card driver, up until the point where it is transferred via S/PDIF.
This means that there is no inherent difference in sound quality between different S/PDIF interfaces. The quality gain you get from connecting an amplifier via S/PDIF over RCA instead of sending a traditional analog signal over RCA/jack cables is so huge that it would outweigh any marginal differences between different S/PDIF implementations.
Thus, when looking for an external sound card that offers S/PDIF—and you are able to use this as an output option—you almost can't go wrong.
The actual quality is determined by the receiver side, because it will convert the digital signal to analog.
In very critical applications (like in recording studios), you'd have to make sure the receiver follows the bitstream by synchronizing to the source clock. This is somewhat explained here, but in practice (e.g. in home theater), I haven't experienced any issues with S/PDIF whatsoever.