Can you please let us know if we can re-program or update the bitstream via USB?
I don't think this info is known (by them) yet. They are likely doing testing on the prototype boards now. Yohan will likely come let us know "All the Juicy Bits" (as he put it) once they have completed testing and have actually hashed on a physical board.
I suspect right now they are focusing on getting it hashing. If they then have time/resources to complete/test additional features and still hit their shipping timelines, they likely will.
My understanding right now is the hardware is fully capable of it, in that the USB chip itself can directly drive the jtag chain, requiring nothing fancy on the control FPGA at all. But I don't know exactly how they have it all wired. depending on how this is implemented it MAY require something in the control bitstream to drive the JTAG (in which case it's a feature they need to deliberately add). If it's wired up in a way that allows the USB chip to natively drive the JTAG, that means the only real limitation is software for your PC that can talk to that USB chip in the appropriate way, to load the bitstream to the board. (so in otherwords the board will support it fine, but you might not be able to use the feature until someone writes said software for the PC).
Also from what I see, there are 2 JTAG headers. It appears the right-angle header next to the USB is the main JTAG chain for the 4 "Worker" chips in the matrix. The other JTAG header appears to be for flashing the Spartan3 "Control" chip. So chances are because there are 2 different JTAG chains, the USB chip can likely only drive the JTAG chain for the 4 worker chips. And the JTAG for the Control chip is probably "hands off" (unless you have a JTAG cable). So I suspect that bitstream will be fairly "fixed" and considered not user-servicable, but the bitstream for the 4 worker chips will be USB flashable by the user fairly easily.
Also of note, Yohan has mentioned that there is the possibility (but nothing confirmed, ie: hardware can do it, but Enterpoint may not have time to roll the feature out before shipping, who knows if it can be added in future). To have multiple bitstreams stored in the flash. So that you can "dual boot" the boards, or have options like a "failsafe" bitstream. So you can install new ones, and it can fail back to the "factory default" bitstream on it's own for example.
Again, same disclaimer as before. All just my own speculation based on available info. Don't assume anything until it's officially stated by Yohan or other Enterpoint "official" channels.