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Basically, what I'm looking for is a way to use "Select By Color", but I can drag around to select multiple colors. I'm working with a limited palette (with more than 255 colors, so an Indexed Colormap wouldn't help), but I want to find duplicate colors (i.e two colors that are near-identical and should be one color to make the palette simpler), so using a higher Tolerance defeats the purpose I want.

Nothing as automatic as you want, that I know of.

Maybe use some helpers. Add two docks  Pointer and sample points.

The pointer shows the pixel info under the (selection) tool cursor.
Sample points can pre-identify points of similar colour to use. https://docs.gimp.org/2.8/en/gimp-sample...ialog.html

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