The 1x16/2x8 GPU port and 1x4 M.2 port goes directly to CPU, Rest of ports come through the Chipset/PCH/Northbridge/Southbridge/however you call it. The CPU-Chipset link is not real I/O bus coming from CPU die for quite some time. So motherboard brands can't just offer x16 to everyone.

Breaking out full sized full speed buses was possible with PCI and PCI-X because those were real buses bridged to real CPU buses. That's not the case with PCIe.

0: https://images.anandtech.com/doci/17308/hlg-intel-prod-brief...

1: https://www.lowyat.net/wp-content/uploads/2021/08/AMD-AM5-Di...