From: Washington D.C.
For the typical Command scenario, it probably doesn't matter that much.
There's also other different logistical requirements for the Navy/USMC versus the Army and USAF beyond fuel. In very real sense, they have incompatible supply chains. The good news is that Command doesn't do much beyond the 12-24 hour time frame well without some pretty extensive LUA scripting so supply chains aren't really an issue. A good game might be about protecting a supply chain, but exactly what the packing list includes probably isn't important on the time scale you're concerned about.
The other good news is that if a jet is fueled with JP-5, it can take JP-8 and vice a versa. In the end it's all just kerosene with different additives for safety requirements. The constraint isn't about burning the fuels, it's about storing them. That's why a Navy aircraft can refuel from Air Force tankers.
Where would it be interesting / important?
If you were to construct a series of scenarios, assembled into a campaign, it might matter more, however, there are other mays to represent logistics. I believe you can, for example, set the keystore to exchange information between scenarios. That way, if you lost the Navy's jet fuel storage at the SPOD (Air Force, you had ONE JOB!), a future scenario might, for example, have an increased number of aircraft in a "Maintenance" state due to the inability to fuel all the aircraft.