it is important to remember that in general the manufacturer and good airlines have generally had higher standards than the regulator.
This is key. Indeed to quote the regulatory material of a regulator:
Through Delegation the [authority] has access to both a broader range and increased number of qualified certification personnel.
So yes, it is likely, and indeed intended, that the FAA delegates employed by Boeing (or any other delegate) could be more familiar with the details of design compliance within their specialty than the FAA oversight individuals. This is as it should be, as long as the delegate is free to exercise their delegation free of undue commercial influence or pressure. It would be common for the delegate to present the details of compliance to the FAA staff, through their normal interaction.
The taxpayer simply could not afford to employ enough FAA staff to carry out all of these duties, in the same way that the taxpayer or pilot community could not afford for the FAA to employ enough pilot examiners to examine every pilot candidate, the FAA delegates that to pilot examiners, whom they trust to exercise that delegation diligently. As in some many things in aviation, it's about trust.