Can you add a usb 3 boot drive to your benchmarks?
I did update the post with a benchmark I forgot to include—NVMe direct is 10% faster than the NVMe-to-USB 3.0-to-Pi adapter, so there is definite and easily-measurable overhead loss in the protocol translations.
Plus the potential (I don't know... but some people say it could happen) for different weird issues to present themselves when going from PCI to USB to PCI again.