There are a lot of political and national security concerns involved in that. The Air Force wants to maintain three aviation vendors in the industry as a matter of policy, otherwise Boeing and Lockheed are equally capable of making bombers.
Awarding the JSF to Lockheed two decades earlier had similar connotations. Boeing could maintain its aviation capabilities and expertise on the back of its commercial business. For Lockheed, losing the JSF would have meant the end of its aviation unit which the USAF deemed critical for national security.
