You make a great point in this article, which is just because we understand how something works does not imply we have reached limits of understanding of that particular process or phenomenon.
I would rephrase the statement I have highlighted as,
For example, when Einstein finalized the Theory of General Relativity, it enabled a more refined and sophisticated understanding of a lot of Newton’s work.
In order for something to be refined, lots of dross or waste is created. When something is disproved, waste — stuff no longer needed — also is created. Each of ‘refinement’ and ‘disprove’ then create waste. Disprove in my opinion is too strong a characterization of outcome of Einstein’s work. Refinement I believe is a better characterization.