This host system should be not much more than a PCIe root emulator though. This is the level one can get on an e.g. FPGA with custom logic, which implies that a

This host system should be not much more than a PCIe root emulator though. This is the level one can get on an e.g. FPGA with custom logic, which implies that any attempts to insert hardware/firmware level attacks into the actual logic you care about is near impossible to do due to the low-level nature of the custom PCIe implementation.