Airframes that were not fitted were still perfectly safe.
This falsely implies that safety is a static concern - make safe once, always safe. Safety is a relative matter and is not just about the 'inside' issues, but about the influence of the 'external' environment. For example, take birdstrike - windscreen A is safe (prob of catastrophic outcome is acceptable) if you want to operate more at medium to high altitude. However, change your exposure to risk and fly more at low level, then you are more likely to come across a bird that could spoil your day. Windscreen A may no longer be safe (prob of catastrophic outcome has increased) because you have changed the operating environment.
So, as regards tuc's "One hopes they have a Whole Aircraft Safety Case which reflects the In Use build standard, not just the As Built one." there is also a requirement to reflect the 'as operated' situation.
sw