In contrast, Flint having the technology necessary for shrinking Kirk's starship is indeed extraneous - it doesn't naturally flow from his character history (he seems to be living with and out of mankind, without access to extraterrestrial wonders, until he purchases the planet), nor is it in any sort of balance with his other achievements and failures (his technologies can't even keep the Raynas safe from the prying eyes of his guests). But Flint being an experienced flim-flam man is consistent with the character and the technologies - and the trick he does with the starship is pretty much the same as "Ardra" making the E-D disappear.
Why is it a trick? We do not need to know what Flint has encountered (technologically speaking) to accept he has the power to reduce the actual vessel to tabletop model size--particularly since the man already proved his command of advance tech by creating androids so realistic, humans simply accept them as the genuine article.
Furthermore, we must consider his line, "you will know the future, Captain Kirk,"
which means exaclty that: he will place the landing party in the same state of suspended animation as those aboard the Enterprise
. Why lie and/or play a trick about such a power, when the risk of Kirk calling his bluff would be severe (considering how "selfish" & "brutal" humans are--in Flint's opinion).
(in Flint's position) play a trick of that nature, knowing what would happen if Kirk and company acted with violence?
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.