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 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...)
This does not mean that there is no way vendor can backdoor the chip you are getting, but it does narrow the possibilities significantly.