I'm not 100% sure of what you mean in terms of how this would be applied. I can see a number of different possibilities, but I guess you just mean you're looking to have the oval tool just add Red to its area, for example, and a separate use of the tool centered on a different point would just add Green, resulting in different colors in the overlapping area?
I've considered adding blending modes for color, which would be able to handle this sort of thing, but that's a huge feature that would take a while to plan out and implement so not something that I can do now. It'd be for a future major version rather than a quick patch like some of the other requests over the past year.