Uhh, why?

I guess there is some appeal to not needing the FPGA software, but JTAG is ungodly slow. It's not an appropriate means of communication between a mining host and the FPGA at all. I don't think this idea is wise nor useful (except to save the step of FPGA programming I guess).
Because it's what the existing code that fpgaminer wrote was using and it saves trying to hook up an extra cable of some kind for communication, basically. There are already methods of running miners without using the FPGA software if you don't want to use JTAG.
I'm no expert but JTAG is plenty fast enough to deal with a getwork request every 21 seconds or so

There isn't a lot of data.
fpgaminer thank you for the explanation!