What USB to I²S module is the Golden Gate using?
If you're using the older Amanero based one or the "plain Jane" JLSounds, you can try upgrading to the Lampizator "sandwich" master clocked JLSounds one.
Since the re-clocker in the Innuos only re-clocks the USB communication protocol part, the clock and overall USB implementation in the DAC still play an important part in determining USB SQ as a whole, as @ kennyb123 has implied above.
Moreover, your observations between USB and SPDIF SQ seem familiar and dare I say pretty much "universal", as many have come to observe much the same results in wildly different systems.
Please excuse the generalization to follow, but since SPDIF cannot get as detailed as USB no matter what the technology used, I tend to think that if the USB implementation is done properly (both in the server and DAC), the result will be "better" than SPDIF, although maybe not as good as direct I²S.
BTW, I've had the Callisto in my system and it's a superb cable.