Hector Martin has a different analysis:

    This article talks about TB4 vs USB4 but that's a
    red herring. This has nothing to do with USB4 and
    Intel USB4 compliant controllers have the same problem. 

    The real reason Apple Silicon is faster is simple:
    Intel Thunderbolt controllers are *external* and
    bottlenecked on a PCIe 3.0 x4 link to the host,
    while Apple Silicon *embeds* the controllers right
    into the SoC, so there is no physical PCIe link
    anywhere. They connect directly to the much faster
    SoC fabric, so have no such bottleneck.

I can't say whether he's right or not, but it sounds plausible.