Standard OPS: Shortwave radio checks by commercial aircraft, prior to trans-oceanic flights, are so powerful, that thousands of miles away, you can hear these pre-flight checks of commercial aircraft and sometimes the militaries', while they are still on the ground "over there."
The Korean airliner would not only have been using VHF (in U.S. aircpace, especially), yet it would also have been using shortwave radio on any flight planned over the ocean.
Already in the story above, is mention of the level of interest and observation by the Soviets, that they knew of the approach control radio traffic as the "Cobra Ball" neared a U.S. base on its return trip.
Such information methods are also used by the Soviets and the U.S. to track commercial flights.
That's the plan. That's what we are supposed to be doing.
So that we are not surprised by commando assault from such "allegedly commercial aircraft."
We routinely practiced for this kind of attack --- especially expecting it upon any of our (and NATO and SEATO) military airfields around the globe.
The problem for the Russians was not that they had any doubt about the Korean jetliner's legitimacy. The problem was that their own plans call for such an assault on us, and they could not rid themselves of imagining that their plan was being used against them.
The Russians chose to err on the side of protecting their careers.
My theory, however, is that they shot it down to avoid embarassment. I hang out with a lot of Slavs, and they can stand cold, bad food, barking dogs, smoke, rickety tables and hard beds. The only thing they cannot stand is shame. To let the aircraft go would have made their armed forces a laughingstock.
Ogarkov and lots of generals were sacked soon after the KAL incident when a German teenager landed a small plane in Moscow. Case in point.