Custom Ordered Color Palettes in Inkscape

Using the Inkscape Generate Palette plugin you can create custom sorted palettes:

First install the extension – see README with options/instructions. Then restart Inkscape.
Then arrange your colored objects on either the z-index, x location, or y location
After that, box-select your whole palette and use the extension by opening Extensions → Palette → generate.
Then name the palette, select your sorting method, and click Apply.
Finally restart inscape to refresh the palette selection.

Links:

Inkscape Generate Palette on GitHub
Generate Palette Extension on inkscape.org
My Initial Post on the Graphic Design Stack Exchange

In v6.0 you can sort your palettes by the location, however the pull request that adds the ability to sort palettes by a grid has yet to be merged and released. I would expect to have this feature in something like v6.1 when their team gets the chance to do another release.