Did the Navy really have a choice at the time, though? Politically, I mean.

Yes, the Navy can select a higher bid as long as there is justification, and here the justification is long-term value and readiness…but a significant portion of the voting public is incapable of properly weighing long-term versus short-term effects.

All they’d understand—and they’d be helped along to this conclusion by plenty of politicians who just want to use the situation to score points—is, “The government paid twice as much for an aircraft carrier than it needed to!”