I'll take a shot at this...The AGP aperature is an area of memory mapped for use by the 3D Card IF IT IS NEEDED for Texture storage, and only to the extent of Free system memory available for AGP texturing at the time of the AGP request. You do not loose the use of this memory for system requests if the AGP card is Not using it. It's not locked memory space.
All the aperature setting in bios really does is set the upper limit on the amount of memory available to use by the Video card for AGP texture storage if needed.
example... You set an agp aperature of 64mb. The video card is 32mb. If the Video card encounters textures larger than can be held in the Local memory on the video card, Memory mapped to the AGP aperature will be made available to hold textures up to the 64mb limit set, providing there is enough system memory available. I think system demands take precedence over AGP requests.
With todays games, a 128mb video card almost never uses any AGP memory. Almost all the textures can be stored locally on the video card unless your running at high Res w/ 4X anti-aliasing and anistropic filtering on.