As a question: the JTAG interface using the FTDI chip uses the default VID/PID, which is rather annoying since it conflicts with existing drivers (I just wasted a while getting this working). And to install the "proper" drivers means other FTDI devices might now pick up the wrong driver.
Why didn't Intel use their own VID/PID pair, program it into the FTDI chip, & then provide unique signed drivers? The only reason some tools don't do this is the minor cost of acquiring a USB VID + signing certs. But I assume this is something that would already exist within Intel for other products.
Fixing on production side would have been < 6 hours (change FTDI script, change PID/VID in .inf files, resign drivers to make new .cat files, recompile any tools that have hardcoded PID/VID searches). Instead this is pushed onto potential customers, and it would be great if this was "fixed" in future versions.
We are indeed already looking into have a dedicated VIP/PID pair for each development board going forward, so as to avoid the issues you mentioned.