In fact, you are both partially correct, yet both partially incorrect.
To get the Apache from Fort Baxter base, you must have completed the final mission (the one where you kill Sonny Forelli). Before this point the Apache will not be there.
If you go in there wearing the cop outfit, the soldiers will not shoot you down.
Completing 100% has nothing to do with it, in fact, by the time the last mission is complete you will typically have around 45% depending on how much else you have done on the way,
Hope this helps?