Description
Yes, when selecting External PLL mode on the Native PHY Megawizard™ for Arria® V GX and Stratix® V GX devices the tx_pll_refclk port remains as a useable port in Quartus® II software versions 12.0 SP2 and earlier.
Resolution
In external PLL mode you should only use ext_pll_clk port and leave the tx_pll_refclk port unconnected.
This issue will be fixed in a future version of the Quartus II Software.