How does the search word highlighting work?

If I search for a word in Atom, then go to the inspector by [Ctrl]+[Shift]+[I], I see no mark-up for the highlighted word/characters.

How is this visual selection achieved, and can I customise it in style.less?

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The decoration isn’t integrated into the display of the text, but lives on a different layer in the page display. find-and-replace creates markers and then dictates what should appear at each of those spots in Less. If you want to change the color, you can throw that same rule into your personal stylesheet.

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Thanks! atom-text-editor .find-result .region selector worked.

So, there is no easy point-and-click way to see the related structure and elements for these other layers?

No easy way, no. If you learn how the display parts of Atom work, you can figure out where to look, but it’s definitely a skill that needs to be acquired (and one that naturally conjoins with knowing how to write a package that changes Atom’s display, if that’s something you find valuable).