VCCH_GXB when Tranceivers not used

I am not using the Transceivers on my Cyclone IV GX150. The pin connection guidelines document has a note (23) that says: "If none of the transceivers are used, VCCH_GXB, VCCL_GXB, and VCCA_GXB can be tied to ground." I ran my design through Quartus 12.1 and the pinout file tells me to tie these lines to 2.5V for VCCH_GXB and VCCA_GXB, and 1.2V for VCCL_GXB. Should I just ignore this or is there a way to tell the software tool that transceivers will never be used so that I will not keep seeing the pin with voltage in the post-fit output pin file. When I see two conflicting statements, it makes me nervous as to which is correct.