There was a previous discussion about pad openings. I can't find it right now, but from what I can remember, we decided to set the minimum pad opening to 40um, as that is what is stated in the guidelines. @Tim 'mithro' Ansell?
As for CUP, we actually wanted to disable the CUP rules during submission (if possible), as this would simplify things slightly because a number of rules would not be applied. However, I don't yet know if we can simply disable/waive the CUP rules, or if they are automatically activated if you have devices under/near your pads.