What input best depends on how well each interface optimized. The Harmony usb interface nothing special so its very possible I2S will provide superior sound quality. In my case I was using Sonore OpticalRendu with Audioquest Diamond usb with Harmony at first. Later went to OpticalRendu feeding Denafrips Gaia usb, Gaia to Harmony via .5m*Tubulus Ximius, Harmony sync'd to Gaia's superior I2S clock.
To really take advantage of I2S potential, one should have highest quality OXCO clock in streamer or DDC vs dac internal clock, so superior timing via syncing to the external clock. Also keep I2S cable short .5M or less, longer cables throw off timing defeating much of the advantage of the external clock.
While the Harmony was nice enough via usb, going this particular I2S route really upped the game, greater resolution, transparency along with more analog like presentation.