It depends on the actual implementation of the chipset and mainboard. Most current ATA (include SATA)controllers are built into the southbridge which bypasses the limitations of the PCI bus (They connect direct to the link that connects the southbridge to the northbridge). (From about the i8xx chipset this has been true). If however your using an add-in controller card then, yes it still is limited by the PCI bus.
Most onboard SCSI controllers are still tied to the PCI bus, but then again I haven't seen a normal desktop board with an onboard SCSI controller still ASUS released the P2B-S. Server/Workstation boards generally tie the onboard SCSI controller to the PCI-X bus, so bandwidth isn't a problem.
I researched what you said, but (correct me if I'm wrong) it was not until the southbridge ICH7 revision that the bandwidth problem went away (about 9 or 10 months ago).