As far as the FPGA is concerned there are 2 kinds of inputs: 1) Differential Manchester encoding for S/PDIF, AES3 and TOSLink inputs and 2) I2S for the HDMI I2S connectors, USB and the Bridge. There’s no intrinsic difference between inputs in a given set: they share identical code hooked to different wires.
With the new release everything will sound better, but if your Bridge II sounds better (or worse) than another connection on older software, it probably still will on the new software.