Don't you just hate it when you ask a question and find the answer just minutes later? Used to happen to me all the time, haha.
I think you can work out the amount of overdraw by looking at the number of pixel shader invocations (PSInvocations), if it's close to the number of pixels in your render target that were covered by geometry (hopefully all of them) then overdraw is about 0%, if it's much greater then you get more overdraw... Another method but which is only really useful for debugging is to maintain an overdraw buffer which you increment each pixel by one when its pixel shader gets invoked, this'll give you the exact number of pixel shader invocations per pixel and you can investigate overdraw issues. Though there's probably a better way to do this.
“If I understand the standard right it is legal and safe to do this but the resulting value could be anything.”
Thanks Bacterius, you're right it'd be relatively simple to jsut compare the number of Pixel Shader invocations to the number of pixels on the screen to check for overdraw.
I also like your idea of an overdraw buffer for debugging\performance analysis. I'll have a think about that some more.