I'm having difficulty wording what it is I want to accomplish, but I'll try to explain. Let's start with the images below:
Image (a) shows the image as I have it right now, with the proper transparency for the topmost layer. What I would like is for the darker rectangle not to show the angled rectangle behind it, like in image (b), but without breaking the path into pieces (and without the additional stroke next to the upright rectangle. It's not clear, but if you look at (b) closely, the dark rectangle still is transparent.
The catch, is that there won't be one angled rectangle, but many, each with varying degrees of opacity. I only want the topmost pixel to show through for each shape, though. I also need to be able to change it flexibly, so copying each shape into a clipping group for each layer below it would be really cumbersome.
This seems like this should be a compositing mode or something, but I don't know what to call it, or how to do it (if there is a simple way. Also, I'm using Illustrator (CS5).
Since it seems my motivations aren't entirely clear, let me explain some more. The image is going to be used in a UI for the Cocoa environment. It's going to be a template image, which means the only color used is black. The only way to introduce shades of gray is by varying the opacity. That's why I need what seems like such a strange constraint.
I updated my images to better reflect the transparency problems. The bottom layer is now also transparent. The only chroma value in both images is now Black, at varying opacities.