> This at a time where metal fatigue and structural load was not well understood
You're mixing up problems that are completely irrelevant to the issue. Fatigue is only an issue in high load cycles (typically over 10^6) which means that it becomes a problem only after years of significant commercial operations.
Running a prototype is, obviously, not the case.
Moreover, structures designed to meet fatigue requirements are designed so that ultimate load is far higher than operational loads (over 5 or 10 times), and ultimate loads are covered by their own design scenario.
Fatigue and ultimate loads only cause problems when aged structures (i.e., planes that were well used and reaching their design life) are subjected to loads close to their ultimate load. That may lead structures to fail when subjected to loads that, although higher than typical operational loads, are far from the expected limit strength.
Here's an example of a retired C130 being used in firefighting missions that gets its wings to break off mid-flight.
https://www.youtube.com/watch?v=PK49QALNj-0
Running a prototype is, obviously, not the case.