Speculating: Yes, but it's probably a bit harder to make a backdoor in an FPGA that can anticipate and manipulate a custom design. The backdoor would have to be smart enough to know it's running a CPU, although if it could just detect that it's running multiple Ethernet ports, it could still act as a silent forwarder for evil packets or a data mangler. It could conceivably also try to send the FPGA design to the backdoor's owner for them to tell the backdoor what to do next.
