I agree that the current paint voxel tool is essentially useless.
It is better/easier to do the same task with a simple cut and paste.
Highlight and copy a region of the same size as the thing you want to color, then scroll up or down to choose the material you want, then just paste it back on top of the original. (not shift paste, just paste.) Because this game has existing dominance, it will simply recolor those voxels with the new material, and won't change the shape.