Pi has limited PCIe lanes to devote to additional controllers. PiBox lacks USB3 for this reason -- all the throughput is already filled by SATA3. 2.5Gbit is likely to be mutually exclusive to either.
not sure it's just a throughput question... the thing is, there's only a single PCIe lane exposed, and multiplexing it to multiple devices (i.e. a SATA controller plus a USB3 controller) requires more electronics, and of course the bandwidth will have to be shared between the devices