I have an update on this.
I double-checked my settings and found that
a) yes, there ARE two boxes for inverting the Y-axis; one for normal play and one for the dragon form, and
b) I HAD inverted the Y-axis for the dragon form.
As I remember it, this did not in fact change the actual gameplay. So either I rembember incorrectly, or there may in fact be a problem.
I'll wait and see what happens when I actually get my dragonshifting ability. I figure that if there had been a real problem with this, chances are that someone would have remarked upon it long before this.