Given the simplicity of the RPi system, it's quite possible that the PCIe bus is clocked from the same source that you are raising the frequency of to overclock

Given the simplicity of the RPi system, it's quite possible that the PCIe bus is clocked from the same source that you are raising the frequency of to overclock the CPU. Since we saw a ~15% increase in NVME performance with a ~33% increase in CPU clock, I'd even go so far as to say that the 100MHz clock to the PCIe bus is somehow derived from the base clock in a way that means that any n% increase in CPU clock would yield an n/2% increase in PCIe performance. This tracks with USB not seeing an increase in speed as that's likely clock stabilized separately.