I assume the same thing, but were not sure.
As you say, this would be an Apple and iTunes thing. As long as it are no separated apps with different names, this should work.
If you set up renditions properly, your customers will be entitled to the same issues on the iPhone as on the iPad. However, if you just create iPad folios, they won't appear on the iPhone, which displays only folios with a 3:2 aspect ratio.
To set up renditions, see this article: http://help.adobe.com/en_US/digitalpubsuite/using/WS9293e1fb3b977c5c-2337961812e35738f56-8 000.html