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.
Not necessarily. The ability to feel romantic love was in Rayna's programming, so technically, Flint was successful all along. His problem was not lack of ability, but the fact
he was not "that guy" in her eyes, and never would be--essentially what Spock told him when referring to Flint as a teacher/father.
So, Flint's power cannot be downgraded to limit the Enterprise event as some sort of trick, as it would make no sense for Flint to threaten to place the crew in suspended animation--in miniturized form--if he could not act on it.
To bluff and not be able to back it up would place his life in great danger.
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?
He was desperate. Initially, he did not want the landing party around, but he had to be honest with himself--slowly--that Rayna's lack of romantic feeling was his problem, not hers. With so few (or no) visitors, why not use them as the experiement to play with Rayna's "heart strings?" He ws not going to leave his world to seek gi
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.
...which was accomplished with the suspended animation effect, not trickery. Reiterating, with so much at stake, it would have been foolish for Flint to threaten something he could not carry out, not only for fear of revenge, but the threat to Rayna; he hardly trusted Kirk & the others, so imagine his legitimate fear of a ship of 430 marching down on his hideaway--a real possibility if he lacked the power to control/stop the ship at will.