The Seattle times report[0] that the delegation was largely politically motivated in an effort to save time on the certification so that Boeing would not be left behind with respect to Airbus.

So it is not a competency issue, so at best it was mostly capacity related: the FAA didn't have enough resources to certify at the speed Boeing needed. Of course, the fact that you are certifying yourself might also speed things up for other reasons than purely your willingness to allocate more resources.

[0]: https://www.seattletimes.com/business/boeing-aerospace/faile...