'Unique', how far you've come

Merriam Webster's Online Dictionary gives the following definition for unique:

1 : being the only one : sole "his unique concern was his own comfort" "I can't walk away with a unique copy. Suppose I lost it? — Kingsley Amis" "the unique factorization of a number into prime factors"
2 a : being without a like or equal : unequaled "could stare at the flames, each one new, violent, unique — Robert Coover" b : distinctively characteristic : peculiar 1 "this is not a condition unique to California — Ronald Reagan"
3 : unusual "a very unique ball-point pen" "we were fairly unique, the sixty of us, in that there wasn't one good mixer in the bunch — J. D. Salinger"
synonyms see strange
— unique·ly adverb
— unique·ness noun
usage Many commentators have objected to the comparison or modification (as by somewhat or very) of unique, often asserting that a thing is either unique or it is not. Objections are based chiefly on the assumption that unique has but a single absolute sense, an assumption contradicted by information readily available in a dictionary. Unique dates back to the 17th century but was little used until the end of the 18th when, according to the Oxford English Dictionary, it was reacquired from French. H. J. Todd entered it as a foreign word in his edition (1818) of Johnson's Dictionary, characterizing it as “affected and useless.” Around the middle of the 19th century it ceased to be considered foreign and came into considerable popular use. With popular use came a broadening of application beyond the original two meanings (here numbered 1 and 2a). In modern use both comparison and modification are widespread and standard but are confined to the extended senses 2b and 3. When sense 1 or sense 2a is intended, unique is used without qualifying modifiers.

Generally, I'm in agreement, but the following from the New York Times, gave me pause:

The organ, the Craighead-Saunders, is a unique instrument, not only because of its lovely sound, but also because it is a nearly exact copy of a late Baroque organ built by Adam Gottlob Casparini of East Prussia in 1776. The original stands in the Holy Ghost Church in Vilnius, Lithuania.

I suppose one could argue that it is the one and only copy, (i.e., that the original is not a copy), or that being only a "nearly exact copy" it had no twin, but were either of these blanched meanings really the one intended?