Thunderbolt is its own protocol, electrically incompatible with PCIe. Its purpose is to encapsulate data traffic from multiple other protocols (PCIe, DisplayPor

Thunderbolt is its own protocol, electrically incompatible with PCIe. Its purpose is to encapsulate data traffic from multiple other protocols (PCIe, DisplayPort, USB) and multiplex that over the same wires. It cannot function exactly like an external PCIe port because it's solving a bigger, more complicated problem.