I think Jefferies well understood the requirements of designing a set for film or television, but he managed to design things that managed to transcend those limitations. He obviously went beyond "slapping some paint and blinking lights together" for a sci-fi look. He did it well enough that he's been emulated for decades afterword.
He reasoned out where things were, where things should go and how things supposedly worked even if it was all fictional.
Didn't he design the phaser pistol? That design looks like nothing that had ever preceded it in science fiction in the visual mediums and it's still a very cool and distinctive bit of SF hardware. I'd have loved to see him create an updated version of the phaser rifle for the TOS era.
His design of the Klingon battle cruiser was another inspired work. The adversary's character was instantly telegraphed in this beautifully menacing design. Before the Klingon warship menacing enemies in sci-fi flew simple flying saucers or versions of rocketships like in Flash Gordon.
The Klingon ship was a first just as much as the Enterprise