That's one way to look at it. One I have no trouble with. An easy way for me to consider it is to say that Tolkien worked on a single, great painting his entire life and portions of the canvas were reworked, repainted, added, or left out. The various notes Chris found reveal the canvas in stages. The published posthumous material attempts to show how the various layers of the painting relate to one another.
It's hard to say what kind of good a definitive canon for Tolkien would do. Fans would still ignore or critique the parts they don't like and filmmakers will simply rewrite it the way they want to anyway.
I think what Christopher has done with his father's notes is about the best we can hope for: an accumulation of the source material that will allow us to enjoy JRR's writing and invention as if we were to watch over his shoulder as he wrote it.
Which is why I enjoy The Silmarillion a great deal, even if it is not, in Mr. Martinez' opinion, "canonical: the wonder of JRR's invention and the splendour of his writing are still there for us to enjoy. That wonder and splendour are lost completely when Mr. Martinez tries to parse it for us to establish his canon.
I don't think he's proposing rewriting Tolkien to establish a canon, but rather pointing out the consequences of an attempt. There was so much work Tolkien did behind the scenes in producing his completed works, that any attempt to bring his more incomplete writings into a canonical framework would take several lifetimes. He was given only one lifetime, and we should be grateful for that.
There is so much wonder and beauty in The Silmarillion that I feel it's better just to have it, as non-canonical (in parts) that it is, than to never have had it written in the first place. Who knows what wonders might have been produced if Tolkien came to fame (and fortune) twenty years earlier than he did?