There are inherent technical differences using RCA coaxial, BNC coaxial, TOSLink, USB (of various types), and AES/EBU for digital audio transmission. But, independent of that, there are also implementation and as a result sometimes audible differences between the connection types when used with a specific product.
The OPPO HA-1 I'm using right now is obviously better via USB from my iMac than via TOSLink. Despite having whatever goodness the ESS Sabre chipset is supposed to provide to address potential signal issues.