The Intel B560 series and 10th generation CPU is considered to be a pretty good deal for some users. One of the 10th generation drawbacks is the lack of PCIe 4.0 lanes. The 11th generation Intel Rocket Lake-S having 20 PCIe 4.0 lanes and the 10th gen has 16 PCIe 3.0 lanes. Each M.2 slot uses x4 bandwidth. Usually, the motherboard uses the PCIe lanes from the chipset. It works via a switch that detects the CPU and allocates the PCIe 3.0 lanes from the chipset.
Therefore naturally, you will assume there would be step-down support for M.2 slots with PCIe 3.0 lanes when the 500 series motherboard is paired with an Intel 10th generation CPUs. However, some motherboards do not have switching support. Since these motherboards have at least two or more M.2 slots, lesser PCIe lanes would affect somewhere. In this case, the second M.2 slot. That was the case with the B560M-A Pro, B560M Pro and the B560M Pro-E. Two of MSI’s motherboards have the first M.2 slots exclusively for PCIe 4.0 lanes with the 11th generation CPUs, but provide PCIe 3.0 lanes on the second and the third slot.
Why on these B560 motherboards? Its likely MSI didn’t provide switches for the PCIe 3.0 to keep the costs of the motherboard down.
Disabled ports for older gens, not a new drill…
These are usually mentioned in manuals, irrespective of the manufacturer, model and the platform. But it does get lost in fine details. This was no different from the time some M.2 slots on older generation motherboards used SATA instead of PCIe lanes. Therefore, one or two SATA ports is disabled if the M.2 is used- and vice versa. One of the implementations on the 11th generation (though not a selling point) is the 20 PCIe 4.0 lanes from the CPU. While it doesn’t make any difference on currently available graphics cards, it does provide ample legroom for mid to high-performance PCIe 4.0 M.2 drives. It’s a question of which M.2 controllers can take advantage of it.