I just spent a lot of time looking into this. I've used Photoshop to copy semi-transparent textures for some time while prototyping (with the destination of Axure RP).
Now, I've tried using the new clipboard API in html 5. I dissected the PNG files that are generated by this process.
If I use the clipboard (with a rectangular marquee) to copy a semi-transparent texture to the browser with the clipboard API, it sets the alpha byte to FF (completely opaque).
If I use the drag and drop API to copy a "Save as Web" PNG 24 file to the browser, it works as expected and transparent pixels work (and the alpha byte is not forced to FF).
Note: Even thought Photoshop says it's 24 bit, it actually exports it as 8 bit still (confirmed).