My personal advice is to continue using USB from the Pi to the GD DI-20 going forward.
As well as the clock issues inherent with using SPDIF, the SPDIF interface is unable to handle PCM over 192KHz at 24bit.
The USB interface is a lower noise, higher bandwidth interface and allows your GD DI-20 to natively handle PCM upto 24/384 and upto DSD512 (which SPDIF is also unable to handle).
As well as the clock issues inherent with using SPDIF, the SPDIF interface is unable to handle PCM over 192KHz at 24bit.
The USB interface is a lower noise, higher bandwidth interface and allows your GD DI-20 to natively handle PCM upto 24/384 and upto DSD512 (which SPDIF is also unable to handle).