...In any case, there is no technology level inconsistency in the Gideonites being able to (and willing to) build a replica starship as a necessary part of their scheme. They lacked in personal space, but they obviously had formidable technologies and industrial capabilities in order to be able to keep the tightly packed megacities stocked and fed. They were just prisoners of their religious mores, and could not use these technologies to pursue their goals in more direct ways.
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.