I think it's reasonable to say a PCIe 3.0 x4 attached thunderbolt controller is bottlenecked by the host attachment; but that doesn't much matter if you're using PCIe 3.0 x4 mode (+/- interleaved display port). And it's also not limiting if you're in USB3 mode.

There's only a real issue with capacity if you're using USB4, so I don't see how it's a red herring. Also, I've just read that Thunderbolt 3 has a hard reservation of 18 Gbps for display port data, limiting other data to 22 Gbps, so comparing TB3 to TB4 in pci-e mode will have that caveat as well.