If you read it carefully, they are saying that if the airplane did land inside their country, it happened with full awareness of the military.
The airplane could circle around India, far enough from the coast to not be seen by radars, and then cross the border anywhere at Pakistan's 500 miles long coast.
To add to the conspiracy: since Pakistan has its own fleet of similar airliners, Pakistan could have filed a flight plan ahead of time. Then the hijacked airplane could switch identifiers to the ones of that flight - and every radar would see it as the scheduled decoy flight, which never left the ground. Alternatively, they put the decoy airplane in the air and hide the stolen one in its shadow. Hard to do that without anyone in the other airplane noticing; but if they are assisting you then it's easier. With one airplane's transponder working and answering, nobody would give a second thought to the double blip on the screen - even if anyone cares to look. If the radar operator is not deeply involved in managing that flight, he won't bother. Other pilots could have seen the unusual pair... but not at night.
The path from Malaysia to Karachi over water is 3,700 miles. A Boeing 777-200ER has range of 8,892 miles, so it's just a matter of fuel. But you know what is the straight line distance from Kuala Lumpur to Bejing? 3,600 miles! Bejing is at the very north of China. So the aircraft had enough to reach Pakistan even without loading additional fuel. At cruise speed of 560 mph it would have taken 6 hours from the moment of departure; the last satellite contact was at 8:11, and that's probably the time when the airplane was completely powered down inside a hangar, or just placed inside a hangar - the steel walls would block the radio signals.
I read an article saying that 370 shadowed a Singapore-Barcelona flight and then peeled off when it got to where it was supposed to land. Possibly Pakistan or one of the other ‘Stans.