The Thunder is already over the cap thanks to the contracts of Durant, Westbrook, Ibaka and Perkins. They are very close to getting in the penalty. If they are over the cap/penalty for 3 years out of 4 - the penalty increases exponentially. That is not a concern for a large market team like the Knicks, Lakers, Brooklyn, etc. But for a small market team, the increased penalty is very scary. The Thunder are staying beneath the penalty for the 2013/2014 season, will likely amnesty Kendrick Perkins before the 2014/2015 season, and then will be over the cap/penalty for 2014/2015 and 2015/2016. After that, they will likely have to let another one of their core players go and hope one of the newcomers can step up.
I'm wondering if you missed this line:
there is a rookie cap exception that allows a team to sign their rookies to the scale even if it goes above the cap line.
Plus even if he signed for 100% or 120% they would still be under the cap as they have more than a million to work with.