Traditionally, one example is software that supports theming. Site owners who wanted to customize the look of something without getting their hands too dirty writing a whole new theme may duplicate and heavily modify the CSS from an existing one.

For applications people spend a expected to spend a lot of time in, the user may even be able to select the theme.

But, things like CSS custom properties have eaten into some of the basic use cases like palette swaps, assuming they're supported in the default theme.

Absolutely. When I first started building websites in the early 2000s, I was building site networks, where individuals would want their own themable websites quickly spun up. They all used the same backend system and components, each with unique designs and custom stylesheets. This pattern is incredibly common, and a lot of themable website building platforms are built on it.

Light theme and dark theme?

I'd say mobile and desktop (from same html) would be more like css zen garden, than light/dark.

Those are palette variations, not enough Zengarden-like

Don't know why this was downvoted, it is the only zen garden like example I've come across. Multiple completely transformative CSS themes for user selection, not just light/dark/colourisation of the same layout