But the thing is, if Flint really has this power, then it's not plausible that he would have to struggle with making a perfect android, or making Kirk stop bothering him in the first place. Flint has to be physically vulnerable, and a man who can shrink starships is invulnerable to the extent of divinity.
Okay, so perhaps giving a tender soul to the perfect android is difficult in the TOS context. But why doesn't Flint make the heroes disappear when they first intrude, or send their ship away when it first tries to make an approach? Yet even if you don't have the power, you can always arrange for a demonstration - North Korea could give some pointers there. It just calls for the perfect setup, so you have to tolerate the guests until your demonstration is ready.
Finally, for the audience's sake, we see what the landing party cannot: the ship vanishing from orbit--proving that Flint's power was not trickery or illusion.
But that's the same trick Ardra pulled, and making it look as if the ship vanished is essential for making the people outside the ship scared. Spock still has his tricorder, Kirk has his communicator; the ship has to be made invisible and inaudible to these if the ruse is to work.