Of course, odds are that Flint never shrank anything. All that really happened, as far as we can tell, is that Flint jammed communications and then frightened Kirk with a detailed tabletop projection of his ship.
I think this is unlikely, because there is a POV shot from the frozen bridge crew, with the main viewer showing life-size Kirk. The suggestion (perhaps the intention) was that the crew might be suspended yet aware of surroundings and passage of time, perhaps like the experience of the Garrard character in the early part of James Blish's story "Common Time."
As for the absurdity of Flint's being able to actually do this - it's no more absurd than (as I wrote earlier) Spock knowing for certain
that the waltz was not only ostensibly by Brahms, but "in Brahms' own hand which I recognize." Or, to take another mid- to late-third-season episode, the Gideons knowing how to build a 1:1 scale-model Enterprise good enough to fool its freakin' captain - a feat that would be next to impossible even for a Federation member planet. Perhaps D. C. Fontana's successor as story editor just didn't give a crap?