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The article presents this idea specifically because it is incorrect, and goes on to explain the newer, more accurate understanding of genes, which is (as far as I understand it) that they encode various options and patterns that can be leveraged by the organism in different situations, not a rigid plan to be executed by the cells.

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I don't understand why that is supposed to be a "new understanding". I think it was the understanding all along (or at least most of the time).

Isn't even the famous moth that changed color in the early days of the industrial evolution an example? I think it carries both genes (for black and white expression), and they get triggered depending on the environment during development. https://en.wikipedia.org/wiki/Peppered_moth_evolution

I could be wrong about the moth, but certainly, genes that are only expressed depending on environment are common knowledge.

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