Well, that's another terribly unrealistic aspect of the episode. The complexity to essentially teleport a vast starship from orbit into a miniaturized form on the surface is... well, just plain ridiculous. Matter must be conserved--so where does it go, and then return from when the Enterprise is restored? Think of the scale of one human being to the Enterprise. The ship was reduced to no bigger than Kirk's behind. And if Flint has that kind of power, why wouldn't he just miniaturize the landing party and then deal with them on that highly advantageous scale of intimidation (e.g. Giant Apollo in "Who Mourns for Adonais")? Anyway, even accepting the outlandish teleportation and miniaturization ability, I suspect it requires line-of-sight to work.
It's all based on sworn testimony. Come on, guys. Play right.
And I cannot subscribe to the idea that Flint was faking the ship capture, not because we see it disappear in space, but because that would make Kirk and Spock out to be fools. Such a capture must be possible in the STAR TREK universe if they accept it as such.
But what is seen on the tabletop could still be a mere representation of what Flint accomplished. Like say the actual ship is suspended in Flint's transporter buffer, and a holographic image of it is presented for Kirk to see. That solves the matter-conservation problem, or it saves Flint from needing a table that can hold 70,000 tons.