Why should it? It's not ram, and the aperture is marked as reserved while doing PCI resource assignment/reservation.If you ahve a proper e820 map, then it should work correctly, with anything that is RAM being marked as such (or being marked as "reserved").
Every e820 map i've seen did not have the AGP aperture marked reserved.
It is just an undescribed hole. In fact when you mark the aperture in the
e820 map the Linux AGP driver stops working, it relies on it being
in an undescribed hole.