As a practical matter, I'm not sure the Mansfield amendment affected all agencies equally. My impression is that it affected ARPA (later DARPA) most profoundly. (pretty much everything I've read about this was in the context of ARPA and XEROX Parc so my perception might be a little skewed)

I'd speculate the Navy had perhaps more discretion over how it spent its research funding. For example, they funded polywell fusion research for years.