HELLO. SATA 3 is 6GBPS.
I know the PCI-E x4 is from the southbridge that means the PCI-E x16 is used for the GPU itself and it can only be used if the GPU is disabled
but you can't have more then one device on the x16 and that's the Q45's limit unlike the southbridge's x4 which can be reconfigured for 4x1 but that's not the case since physically the x4 is there for an upgrade for a high-speed offloading module from Agilent
which definitely points to a SATA 2
As monkeh pointed, you made an order of magnitude error in your units for SATA, SATA3 is 600MBPS (that is, MEGABYTES)
Also, you're wrong on the limit, the pcie lanes from the root complex have NOITHING to do with the GPU, the internal GPU is disabled ONLY if you attach another GPU to the system(that is ANY GPU IN ANY BUS, if you put a pci vga, it will disable itself) and that's a limitation of the GPU.
the lanes are normal pcie lanes which can be used REGARDLESS of the internal GPU.
And as i've said before: i've tested that myself
i.e.: grab any normal PC with integrated graphics, plug a pciex1 device(usb adapter, soundcard, sata controller) into the pciex16 slot and MAGIC, it works!