Arrow-USB-Programmer should be fully compatible to original USB Programmer with the exception that only JTAG mode is supported. Pin-out is compatible, JTAG Voltage range is limited to max 3.3V. JTAG interface on most Intel(Altera) based boards is designed so that the original USB-Programmer cable when inserted goes away from the board, same with Arrow USB Programmer2, when inserted so that USB cable goes away from the PCB then it is correct. Pin 1 in the 2x5 Female header is also marked with white dot.
One time installation of Quartus support libraries is needed. There are no custom USB drivers needed, WHQL certified Drivers from FTDIChip are used.