Do not they having cushons, overprovisions, dummy weights, tolerance ranges to account for unexpected spec changes?

I imagine the systems are very complex, so the components are made modular, defining functionality and specs (size, weight, mass balance) and letting the implementation details to subcontractors.

While the subcontractor fullfills the contractual functionality, any eastereggs can be discovered only in a very late phase (qc, assembly), upon delivery.

The wording "discovery was reported" can be read as if it was a surprise discovery for all.