Right. Who else has the raw logistical capabilities to establish a complete base with water, power, sanitation, transportation, command and control facilities, and security in a matter of days? It's just logistics. Legitimate question though why there wouldn't be a civilian executive in charge of the operations who could be from some other executive agency.
The way I would anticipate it to play out IRL is the President orders the military to set up the base and secure the area. The military provides the personnel and logistics to operate and support the base where civilians will work and live and provide security, but the President would use his authority as CIC to delegate operational command to the office of the director of the NSF or something, basically putting the military at his or her disposal.