If you're concerned about the size of touch targets on the iPad mini, they are already the EXACT same size as the touch targets on an iPhone since the two share the same pixel density and recommended touch target size (40px).
If iPad Minis are served iPhone-specific designs, then you're right—it doesn't matter. And perhaps the solution is "you shouldn't be making iPad 2/iPhone-specific designs," but that's not what I'm getting at.
You're saying that buttons on the iPad mini must be physically larger than buttons on the iPhone? For what reason?
That's why I mentioned an iPhone-specific design, as well. The iPhone's pixel density isn't a problem because it can be distinguished from the iPad 2. And, as you've shown, if the iPhone-specific design is displayed on the iPad Mini then there is no problem at all. The issue is that there is no way to distinguish between the iPad 2 and the iPad Mini.