You're correct in that the FAA can't (or at least, it would be wildly impractical) have a staff of in-house experts that equal or exceed the experience of the manufacturer engineers on every possible topic.
But, that's not necessary to enforce a process of quality. It can be done by enforcing that the company must establish and document the processes to ensure quality, including which experts need to sign off on what. Then the FAA needs to hold the engineers who sign off professionally responsible and their managment legally liable if any circumvention is discovered down the line.