Maybe "U.S.S. Enterprise - Starship Class" was just too concise and therefore they felt it to be necessary to be more specific in later dedication plaques.
I just rewatched the opening scene of "Court Martial" (TOS without R) and we see the Enterprise
just arriving or orbiting but without any repairs being done on her.
I still advocate the "upgrade" interpretation, especially since there is evidence that upgrades were performed (i.e. Stone realized Enterprise
needed an upgrade in addition to the repairs).
Here is the Deck 7 Engineering Control Room from "The Naked Time
". Notice that there are only two
horizontal tubes behind the grating in the "cathedral".
Here is the Deck 7 Engineering Control Room from "Court Martial
". You will notice that now there are three
horizontal tubes behind the grating.
Since this upgrade is obvious, there is no reason to doubt that Stone was looking at an upgrade status chart and the still to perform upgrades on the Enterprise
were not yet "complete".