It's not just the controllers; the Thunderbolt protocol itself imposes different speed limits. The bit rates used by Thunderbolt aren't the same as PCIe, and PCIe traffic gets encapsulated in Thunderbolt packets.
Maybe; I'm unable to find any benchmarks that specifically compare PCs with TB to Macs to test this. But there is certainly still overhead with TB no matter what, and therefore it'll never be as fast as Oculink.