But how come I2S is still not the digital standard for a CD transport and DAC interface
Mostly because it does not provide copy right protection, and other user programmable features.
As I mentioned, I2S is just one of the standards a DAC chip can take, such as MSB and LSB, but let's focus on I2S as you know it.
I2S contains 4 signal lines; data and 3 clocks. S/PDIF contains exactly the same unaltered signals, less the 4th line, the Master Clock. The real fault of S/PDIF comes from the PLL used to "recover" the Master Clock inside the S/PDIF receiver. This usually results in relatively very high jitter level and poor sound quality.
Providing a high-quality external Master Clock, or re-clocking solves all issues with S/PDIF. In my experience, such solution is not even a bit worse than I2S.
Best,
Alex Peychev