You could have explained your special needs right from the beginning.
Maybe you can use graphic polygons, not zones. KiCad UI doesn’t let you draw graphics directly in a copper layer but you can draw to another layer and change the layer in its properties. If you use scripts you can naturally set the layer directly.
But polygons don’t take any DRC into consideration, i.e. they don’t give way to any other copper features and don’t know about any clearances.
If you want isolated copper areas you could also try zones with no net set.
