Hamster, ATI has nothing to do with the PCI-E support in the linux kernel. That was all code written by the developers of the linux kernel (Linus T.). ATI writes driver code for their video cards, and PCI-E has to be compiled with the kernel if you have a PCI-E card. The PCI-Express code in the kernel works just fine. The ATI-drivers for ATI video cards on the other hand do not work as smoothly with some cards.
Andre, 2.6.x kernel has support for the PCI-Express bus. It works fine. Enjoy