Is the idea that all of the software in the kernel to interface with these devices is open source?
I also don’t get the hangup over PCIe (vs USB). DMA with an IOMMU can be made fairly secure (and has obvious perf benefits).
I'm pretty sure no closed source software runs on the CPU. As for the hardware that depends on your definition. Hardware often has firmware in ROM. That you now feed that firmware on bootup instead of it being in ROM just allows you to update the firmware from the manufacturer. If that's running proprietary software depends on your definition.
There's also just more layers of security when using USB as opposed to a single layer with PCIe (IOMMU -- which is secure as far as I know but I'd prefer to be safe rather than sorry in this case).
What’s the difference between a person and a cellphone?
A person only has two arms.
IIRC this is fine even under FSF "Respects your Freedom" rules