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A hardware trojan can be implemented by the ASIC designer team of each part. In this case, you cannot verify whether there is a hardware trojan inside your FPGA or not. You could have verified this if you had designed the FPGA (instead of Altera). A hardware trojan may not need any external device for any thing.
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Well, if one is that paranoid then the only solution is to design the part yourself from the transistor level up using your own libraries. Then generate the masks in your own facility, fabricate the parts in your own fab, and package the parts yourself.
Oh and of course you will have to write all your own place and route tools as well for your custom FPGA design, as you can't trust a vendor to not insert some malicious bits into the programming bitstream.
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