I can understand why you might think the paint might be lighter based upon some of the pics, but I don't think there is any difference.. other than the different factory i.d.
I did put Spyro (still boxed of course) on a GITD Giants portal and it came up Series 1 Spyro and then errored out after repeated attempts. I didn't try SSA, but I'm guessing it would have done the same thing. The packaging is different, in that, it slopes forward when you place it on a flat surface. I think the error is being caused because the RFID is being read at an angle.
--- REWARD: for valid information that leads to the addition of an ULTRA RARE 2011 E3 Gill Grunt in the E3 packaging.