My motherboard provides 4x USB 3.2 Gen1 ports for rear I/O and another 2x USB 3.2 Gen1 ports for front I/O (through the header), but my chipset only supports 2x USB 3.2 Gen1 ports. Where is the support for the other ports coming from?
Nah SATA is built into the chipset. That second x16 is actually only electrically x4 in an x16 form factor, and there's that x1 slot, adding up to 5 lanes in total. The first x16 and first nvme slot (x4) are connected to the CPU directly (which IIRC most have 20 lanes on AM4, but not always).