>That's the result of political contrivances, not any sort of deep connection between the U.S. military and scientific progress.

The DoD sure wants to have a major influence on fundamental research and scientific progress. http://www.defenseinnovationmarketplace.mil/FFRDC_UARC.html

The UARCs are DoD's attempts to have influence into fundamental research and engineering.

Those positive impacts probably are still likely due to political factors like you said, but it isn't for lack of the DoD trying.