Assuming that the SM-3 block 2B makes significant changes in the design, then much of the Raytheon design may not be relevant.
Besides, the Prime Contractor is often not the one who actually builds the pieces, just the one who oversees the process, and maybe assembles the final product. Hopefully the prime has people experienced enough to spot when subcontractor designs are diverging or failing to perform. Even Raytheon worked this way as the prime.
Lastly, if you keep using the same prime then you are likely to get stuck with a NIH philosophy that blocks anything other than incremental improvements in performance (lighter parts and faster electronics for the most part), because they know how it has to be done. If you want a fundamental rethink of the concept (clean sheet of paper) you almost have to get an outsider. And frankly, neither Lockheed or Boeing would really qualify.
As examples I would offer the classic example, the Sidewinder missile, which was not developed by industry, but as a private project at the Naval Air Weapons Station. Another would be the ‘Land Warrior’, which, while it eventually failed, only achieved a critical weight reduction, performance improvement, and cost reduction AFTER it was transferred from Hughes Aerospace to a Silicon Valley startup.
:coffee