I was able to put some spacing (cut strips from anti fatigue mat) under my mounts and get the basket barely high enough to open the sunroof. It still barely touches it though, so I am not comfortable opening unless I can monitor it as it moves. I am using Whispbars, so they are as flush as you can get. If I found a little thicker mat or better yet strips of solid flexible rubber, I might be able to get it up just the perfect height.Thank you Atlas, pictures 4 and 5 are exactly what I needed to see.
All but confirms my thoughts that you wouldn't be able to open the sunroof with the lower flush mounted style crossbars with the basket on top.