As I understand it, the more RAM on a peripheral, the more address space it uses up - e.g. someone with two 8800GTXs will lose 1.5 GB of usable RAM in the non-server 32-bit Windows OS, regardless of the BIOS remapping (well, except the BIOS remapping would have them lose more, from the sounds of it).
If someone has two of the 1GB HD2900XT cards in Crossfire, that's 2 GB of address space right there. Where does their sound card RAM go? Their physics card etc etc? What happens when someone starts using 4-way crossfire? Graphics cards are probably going to be the big problem as they seem to increase the amount of RAM onboard every couple of generations at least.
Hmm... As with other devices, you're still using system memory as usual, putting data there and ask the card where to find it and to copy it to itself, by itself (through DMA). Thus, whatever cards own memory doesn't have to be addressable directly.
When it comes to graphic adapters, I believe they've enjoyed IOMMU since AGP, called the GART (I'm betting you've heard/read that before). It handles the exchange of data between the graphics memory and the system memory, but can do a lot more by itself than standard devices. And I guessing the Aperture Size is the maximum size of RAM that the graphics IOMMU will be allowed to play with. But more importantly, it is allocated only when needed (like playing a game). Or something like that...
Memory mapped I/O on the other hand, which is the problem here, is when the devices registers
(which is how you control them, tell them what to do) is accessable to the system through regular memory addresses, ie. its like they're part of the memory, but writing to them actually sends instructions to the device. The CPU (and you) can use the same way to instruct devices as you do reading/writing to memory.
Bottom line, you don't access devices own memory directly. These register addresses doesn't take up nearly as much space as if you would have to reserve it to address all of the memory on eg. graphics cards and such.
And again, read my disclaimer.