It states in the manual, that if you use the keyless remote to lock the truck, then you must use the keyless remote to unlock the truck.
Using the key in the door will unlock the truck, but also set off the alarm, and I believe it disengages the fuel pump so the motor will crank, but never turn over.

If you use the manual lock on the doors to lock the truck before you close the door, or use the key in the driver's door(since there are no other door key holes) then the truck can be unlocked, using the key without any issue.
The only time the anti-Theft system is activated or de-activated is with the Keyless remote.
HTH