I've actually never said anything like that about the 5970. It is a very long GPU and you need to ensure it will fit in any case. I've never personally used the 5970 in the 690 II Advanced case, so you can only hope for somebody who has tried that combo to chime in. The 5870 will fit, but according to this review the 5970 will not. http://www.pureoverclock.com/review.php?id=882&page=4
I'm not sure if removing the HD bays will allow the 5970 to work or not. Sorry I can't be of more help.
Edit: After looking closer at that review, it looks like removing the HD bays won't help since only the bottom bays are removable. The top two are fixed and those are the ones that would need to be removed to fit a larger GPU.