Sorry to read this situation happened to you. I thought locking the keyfob inside the Passport was almost impossible to do since the vehicle will unlock itself if it detects that keyfob anywhere inside the Passport. Even if you manually lock the doors using the door controls on your way out the vehicle will automatically unlock if Passport detects fob inside. 
Page 143 of Owners Manual states:
■ Lockout prevention system
The doors and tailgate cannot be locked when
the smart entry remote is inside the vehicle.
Perhaps you can take the key from the second keyfob and find a place to "hide" it (magnetic key retainers are readily available)?
Remember that most thiefs also look in those 'typical' hiding places, too.
Page 143 of Owners Manual states:
■ Lockout prevention system
The doors and tailgate cannot be locked when
the smart entry remote is inside the vehicle.
Perhaps you can take the key from the second keyfob and find a place to "hide" it (magnetic key retainers are readily available)?
Remember that most thiefs also look in those 'typical' hiding places, too.