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Yes, but there are some methods to GUESS if your fabricated device has something inside that is not yours. There are also some methods to prevent another team (the fabrication foundry team for instance) from changing or adding something new to your design. This is a field of research. Different approaches may use delay, temperature, power, parasitics, etc to detect a trojan. Nonetheless these methods can be applied if YOU have designed (even with third party tools) your chip.
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But here, Altera design the chip, and the bad guy with the trojan would have no way of knowing the intended board layout or design so a trojan would be rather useless. It would be spotted rather quickly as chips are used by 100s of different customers on 100s of different boards all with different pinouts.
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