Much like the Amphitheatre Nimes is not closer to the original Colosseum, even though it suffered much less damages over the centuries and had virtually no visible restoration (some of the Colosseum ones are quite bad honestly)
The last supper importance is not just the painting itself, but also who originally made it and the history behind it.
The copy was made at roughly the same time of the original, so it is a great reference for how it should look, but the techniques used for the original Last supper are so different that they are very different in terms of its importance and the difficulties to preserve it and the fact that Leonardo made it explain why the original suffered more damages throughout history (it was simply more famous)
Like the Amphitheatre of El Jem, that was used to film The Galdiator, and the original Colosseum.
We're lucky we have an almost exact copy to look at, that's for sure.