I am not very familar with the CJK unification project so take my points with a grain of salt.
> more than not opposing CJK unification, I benefit from it greatly.
I think think that is a different point of view. Isn't it? You are seeing your benefit whereas the author is seeing his. Here's an alternative solution: What if the search engine understood what you were searching for and returned results in all the languages? Unification can result in a lot of information loss the same way a photo can be compressed but it comes at the cost of loss in quality.
> so there is(to my eyes at least) no value in fragmenting instances of the same character.
But no-one is fragmenting instances of the same character. They _are_ different characters from different languages. To take an example from the article, I am not sure how I feel about combining B and β. You are either ignoring the whole of English speaker population or the greek speaking one. Given that you have complete flexibility to assign a code for both of them, why not do it(responsibly)?