You can change a color on a layer by Color>FillObject but this only really works if you have a flat color. Any painted part will be filled with flat color again. Note that if you turn the RGB Intensity down you can fill with “washes” to subtly change the Hue/Sat.
Changing the Hue/Sat is more difficult… if I really need to change the color I will snap the view to an orthogonal use Zapplink and take it into Photoshop and change it. Then rotate to the otherside and repeat. You will probably have to color sample and repaint the area where it fades together. It’s hacky and it sucks but its the only way I know of.
Yea erasing Polypaint with Alt does leave some artifacts. There are still some issues with layers and Polypaint. I am not sure if what you are going to be using the Polypaint for but if you “erase” using pure white (or whatever color is behind it) it doesn’t leave the black artifacts.