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A subverted FPGA could contain a whole different circuit which turns on based on whatever condition desired (timer, radio command, data pattern seen by the FPGA) and takes over the function of the FPGA in whatever way the subverter intended. As the post to which you are replying said, for good effect, the designer of the subverted circuit would need to know the function the FPGA is performing in your device and design a custom circuit for it. This is possible e.g. by examining the first batch of your devices, and inserting a subverted circuit in your supply chain for subsequent batches. Certainly a lot of trouble to go to, but it's possible theoretically, and people have been writing about the possibility.

Now, the FPGA is not necessarily an ideal place to insert your circuit; personally, I would put it in something like one of those flat ribbons which connect components inside so many devices, or a socket - they may have access to all the bus pins of the gadget, and they will be less conspicuous. I don't think 3D printing is the answer to this, since too many things would have to be 3D printed.

Now, I don't know how I would go about protecting from such attacks, or if this is even a real-life concern right now, but I would think that some kind of automated high-resolution X-ray imaging and analysis technology would be a more realistic direction.

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