Does the "removing dead code" advantage outweigh the additional complexity of having to maintain 2 different confusables lists: one for when NFKC has been applied first and one without? It didn't sound like applying one after the other caused any errors, just that some previously reachable states are unreachable.
This is an inexplicable, AI-written article and the obvious answer is no. There's no performance or complexity overhead to not removing a couple of dead characters. There is a complexity overhead to forking off the list or adding pointless special cases to your code.