I don't see the argument as the second painting is the original, just that it more closely resembles what they original may have looked like.
There are some recent art restorations which exemplify how much the art can change. Both pieces together add to the story.
I think that "it's not the original since 1550" it's an overstatement
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.
