Did you see the A-Series Guide? I tried to make it prominent on the front page and product pages, but maybe I need to rethink its location.
As for JTAG orientation, the programmer board was originally designed to be stacked on top of the FPGA, but the SMD header connector worked so much better than the vertical header that I went with that on all the boards.
Power is not provided by the JTAG header because of potential polarity issues you alluded to as well as size constraints. I thought it would be ok since the official programmer cables also don’t provide 3.3 volts. If I were going to start all over on the A-Series I might have done it differently. The programmer board at least has 3.3v output that you could solder a pin to and use a jumper from the programmer to your breadboard.