I'm not sure everyone knew that gaps reflected incorrect reasoning. It would have been natural to assume that all infinite sets were qualitatively the same size, since uncountable infinity was not an idea that had been discovered yet. Zeno's own resolution wasn't that his reasoning wrong, but that our perception of the world itself is wrong and the world is static and unchanging.

As for the importance of visualization (of the reals), I don't think you can cleanly separate it from formalism (as constructed in set theory).

I think we all have built in pre-mathematical notions of concepts like number, point, and line. For some, the purpose of mathematics is to reify these pre-mathematical ideas into concrete formalism. These formalisms clarify our mental pictures, so that we can make deeper investigations without being led astray by confused intuitions. Zeno could not take his analysis further, because his mental imagery was not detailed enough.

From clarity we gain the ability to formalize even more of our pre-mathematical notions like infinitesimal, connectedness, and even computation. And so we have a feedback loop of visualization, formalism, visualization.

I think the article was saying that Dedekind and Cantor clarified what we should mean when we talk about the number line, and dispelled confusions that existed before then.