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To what degree can misbehaving PCIe devices (as in the device as a whole being malicious, not simply manipulated) override IOMMU protections? Can they pretend to be another device or otherwise send unexpected signals to confuse this defense?

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Violating the timing specs for PCI signalling would put the whole system into an undefined state. It's possible you could glitch the thing on the other end into doing whatever you want. Who knows?

PCIe devices can identify themselves to the host with whatever vendor and device IDs they want.

Since PCIe is a point to point link rather than a shared bus, it is not really possible for a malicious peripheral to pretend to be connected through a different port. PCIe switches may weaken this security somewhat.

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