Multiple Palettes from Library
The video above shows how you can import icons from Harmonicons while keeping multiple color palettes. This video also demonstrates IcoMoon's multicolor font (COLRv0) output, and publishing features.
In the library, icons that have already been added to your project are shown with an outline. When the colors of an icon don't match with that of the selected palette in library, a dashed outline would appear instead. Re-importing icons with a dashed outline would result in updating their colors as opposed to adding a new icon to the project.
Harmonicons comes with 4 multicolor palettes. You can switch between these palettes in the library. When you select an icon, it would get added to your project along with the selected palette. If you then want to import other palettes of the same icon while keeping the current color palette, you should first Duplicate it.