I haven't gotten any reasonable answers. The only thing I can think of is the lack of any available stop over locations on the route for refueling, etc. But then, why not refuel them mid-air? Maybe unaccommodating neighbors who refused to allow combat aircraft destined for their adversary through their airspace? I couldn't find any overt hostilities in their neighborhood either.
These aircraft were first completely assembled at Kamra, flown for qualification and testing, then taken apart and transported. They were then re-assembled by Pakistani technicians/engineers in Nigeria. Nigeria would not have qualified personnel to do so. Nor would they want to train any to assemble just three examples. You can see in the pictures that the machines are completely assembled. The wings, tail, etc. were only removed for easier transportation. All of this would have increased the cost, not that I see anyone caring to save cents over tens of millions of dollars.
Furthermore, you wouldn't perform final assembly in an adhoc hanger or test the machines after delivery. The "zero meter" thing is only Pakistani awam's psyche, I hope. It would have made no difference. Pakistan has always flown its F-16s to and from the US.