Would the build not recognize the difference or be capable of supporting the USB 3.0 speeds? If problems arise, would the issue sit with software, hardware, or another area?
Considering the specifics of your question, I think the first thing to mention is that the build will not recognize that a device is capable of USB 3.0, because that concept doesn't exist for the USB chip that the Pi contains.
If problems arise plugging a USB 3.0 device into your Pi, it might be centered around the issue that the device (whatever it may be) might be designed in such a way that it will only function at USB 3.0 speeds (I'm thinking in this case about devices like uncompressed HD video converters -- NOT that such a device would ever be capable of actually working on a Raspberry Pi, this is just hypothetical).
But for most USB 3.0 hardware, they have plugs capable of working in USB 2.0 host sockets (the "A" plug), and are also capable of receiving a USB 2.0 "B" plug into the device itself. And finally, most USB 3.0 hardware will be happy running at the reduced throughput of USB 2.0 without issue.