If the FPGA is a closed-design are we really that better off?
The real question is: Is there anything hidden in the silicon? That's something you can only solve by owning your own fab - the US military approach.
This does not mean that there is no way vendor can backdoor the chip you are getting, but it does narrow the possibilities significantly.
This can be hidden in an FPGA - for example attached to the input pins or SERDES - without needing to know anything about the application.
(Article: https://spectrum.ieee.org/semiconductors/design/the-hunt-for...)