Now if he had assumed the form of some of the shields damaged components then I might have been able to swallow that a little more easily...maybe.
How is this interpretation excluded by the episode?
We only hear Spock speculate on the Vendorian's activities in the vaguest of terms. We don't see whether he exits the ship via shuttlebay (like his original escape plan appeared to have been) and becomes the shield directly or whether he enters the engineering area and becomes the missing component instead. However, because we see him enter the bridge immediately after the combat action is over, without any further mention of shuttlebay door activity, it's pretty natural to assume that he never departed the ship...
The story structure has some weaknesses, though, with all the quick knockouts and impostures one after the other coming off as a little repetitive. It's also implausible that either Spock (who's very observant) or McCoy (who works in sickbay every day) would've overlooked the extra exam table.
Basically, I think that in live action, we would have seen an extremely fast-paced ongoing chase, where neither Spock nor McCoy would really have had time to react to the altered sickbay. The way the animation clumsily portrays this chase, with one character moving and the others staying put, stunned and immobile, is the dramatic weakness that tilts my personal vote to "One of Our Planets Is Missing"... The plotline of that episode was more forgiving to the shortcomings of the animation.