Welcome to SCF. So first of all, none of it is real. SketchUp isn't attempting to perfectly recreate things like transparency. On the other hand, because you would be looking through the blue cylinder twice to see that part of the yellow one, the idea of making the blue more dense in that area makes sense. You might be able to improve the appearance by changing the transparency quality setting under the Edit tab for Styles. You might also find that changing OpenGL settings has an impact. If you are really concerned about creating an accurate representation of the transparency, you should be running your model through a rendering application. They are designed to handle that sort of thing.