I used to have a D90 not so long ago and after your post I went to my collection and checkout out the images. You are right that D90 was different, hence the confusion for me.
I wish if there was a setting in the setup somewhere to switch between old Auto-ISO and new Auto-ISO approach. Accounting for flash compensation seems intuitive to me when camera meters the scene and selects ISO. The new one is pretty useless for me while using flash.