It seems to me that a fixed clipping rect of (0.25, 0.25, 0.5, 0.5) is being used, irrespective of whether you supply your own clipping rect or not. (I've only tested in beta 3). This is surely a bug. Did you raise a radar?
I've seen the same behavior and agree with hacknicity that this appears to be a bug in the iOS Beta. I would also recommend filing a Radar against this.
I saw this too and now with iOS10 GM dove in a little deeper.
UNNotificationAttachmentOptionsThumbnailClippingRectKey does have an effect, but only to crop the photo MORE and you can't use a negative outset to uncrop.To get uncropped photos I'm rendering them 50% bigger... Would like to hear from Apple on this.