It's rather amusing to call the TMP thing "not a normal refit" when ships in the real world do get refitted more or less exactly like that.
Okay, so Starfleet may use the word "refit" (but in TMP, we don't hear this word) where navies on Earth might opt for more descriptive words like "rebuild" or "conversion" (but they usually don't). Yet a century ago, it was quite usual for a navy to take a ship, cut the hull to pieces and add a few meters here, a few there, plus all-new engines, all-new guns in all-new turrets (repositioned, added, removed), a different number of screws and propellers and an altogether different type of powerplant. The end result might have 30-40% commonality with the original, and utterly different looks, performance or purpose.
Granted, this sort of treatment was typically reserved for relatively large vessels, but ships down to destroyer size were involved on occasion, so this tells us nothing definite about the relative status of Kirk's ship. Also, international treaties ITRW may have promoted the recycling of old hulls rather than the construction of new ones, but many conversions preceded both these specific treaties and indeed the very concept of nations agreeing on anything much. In TMP, we can speculate on the role of the Organian treaty, of course.
The rebuilding ITRW very seldom served the ideals of standardizing. Utterly regardless of whether the originals or the end results were good ships or rotten ones, there'd be few of a kind originally and few of a kind ultimately. But testing of a concept through rebuilding, and then newbuilding en masse, did happen - we could easily see a TMP refit of less than a dozen ships verifying the solutions that would then see mass production in the form of
Miranda, say.
As for "only twelve like her", well, if DSC shows us 147 starships on the first season and none are "like Kirk's", then the phrase gets splendid statistical support! (Even better if there's one like Kirk's on the second season, as a desperate publicity gimmick.)
Although of course DSC takes place a decade before TOS or thereabouts. At the loss rate indicated in TOS, there should have been about 20-25 ships "like Kirk's" in operation in the early 2250s...
Timo Saloniemi