There could be, but mustn't it be aware of schematics FPGA is soldered into? A secret block to just manipulate flops isn't enough - it must be able to be controlled by someone.

Well, in theory it must not, because it could detect "oh, this looks exactly like one of popular Ethernet cores, so I'll bug onto those pins and have networking", but this seems like a hard task. Or, well, it could be that every pin is hooked and a secret block awaits a specifically crafted code (somehow like port knocking), but I'm not sure this is a feasible approach.