[toast0]

For Skylake, Intel ran 16 lanes of pci-e to the CPU, and ran DMI to the chipset, which had pci-e lanes behind it. Depending on the chipset, there would be anywhere from 6 lanes at pci-e 2.0 to 20 lanes at pci-e 3.0. My wild guess is that a board from back then would have put m.2 behind the chipset and no cpu attached ssd for you; that fits with your report of the GPU having all 16 lanes.

But, if you had the nicer chipsets, wikipedia says your board could split the 16 cpu lanes into two x8 slots or one x8 and 2 x4 slots, which would fit. This would usually be dynamic at boot time, not at runtime; the firmware would typically look if anything is in the x4 slots and if so, set bifurcation, otherwise the x16 gets all the lanes. Some motherboards do have PCI-e switches to use the bandwidth more flexibly, but those got really expensive; i think at the transition to pci-e 4.0, but maybe 3.0?

[vladvasiliu]

Indeed. I dug out the manual (MSI H170 Gaming M3), which has a block diagram showing the M2 port behind the chipset, which is connected via DMI 3 to the CPU. In my mind, the chipset was connected via actual PCIe, but apparently, it's counted separately from the "actual" PCIe lanes.

[wtallis]

Intel's DMI connection between the CPU and the chipset is little more than another PCIe x4 link. For consumer CPUs, they don't usually include it in the total lane count, but they have sometimes done so for Xeon parts based off the consumer silicon, giving the false impression that those Xeons have more PCIe lanes.