While looking at Validation Reference Platform for 11th Gen Intel CPU (Tiger Lake UP3), I noticed that some pins for the MCP (Multi Chip Package, which is a package that includes PCH+CPU on the same chip), I found out that some pins can be used both as PCIE and USB3. I was wondering how we choose what protocol can be used each time?
Use of configurable multi-purpose pins was there in microprocessor industry for ages. Even simplest MCU as 8-bit Silicon Labs processors have pins that can be openly configured by user's firmware.
Processors of x86 complexity usually have thousands of configuration registers, accessible usually via a secure protocol. Whoever makes a specific device/mainboard with specific use of these nearly general-purpose ports, they use an encrypted protocol within its BIOS to configure these ports in accord with how they are hardwired. Some manufacturers can use these pins as PCIe, some as USB3. These pins are not "used each time", they are used/configured only once on boot, in accord with how they are routed on PCB, to which ports (PCIe slot or USB connector). This hardware obviously don't change on a particular product.
If this is a "validation reference platform" where these pins can be routed to universal (SMA type) RF coax connectors, you need to contact Intel, they might help you (if your product is expected to ship in quantity of ~50k per week). But generally it is not your (customer's) business to conduct processor validation, it is done by manufacturer.