Adding a way to break the JTAG chain would add a fair amount of extra complexity for something I think very very few people would ever use.
I didn’t want to clutter the board with LEDs that just sat there. However, I too don’t like that you have no indication of power if the FPGA isn’t programmed. To keep things simple/pretty, I redesigned the DONE LED to use a dual color LED. It’ll now be red when the board has power but the FPGA isn’t configured and green when configured.