Unfortunately the mobile versions of Acrobat Reader do not display portfolios. Adobe don't have feature parity for some reason. (Actually one reason is that most portfolios need Flash, for some reason, and Flash isn't available for mobile).
I've figured out if you hold down on the file and open with Adobe Reader this works, I'm not familiar with the Apple UI, is this because it is not set up as a default that if you tap it, it opens at the cover sheet?
Ah, so you have a portfolio that does work in the iPad Reader? That's lucky, and unusual.
To answer your question: you cannot change the default PDF app in iOS (iPad/iPhone). Apple just don't let you do it. So you always have to open in the default app, then send to Reader or whatever PDF app you want; or in some cases send from one app to Reader. In theory any one app could do this by default, but none do. There just isn't the Windows/Mac idea of a changeable default app.
Just to clarify, it doesn't work in the Ipad reader you have to hold down on the link and select open with Adobe Reader, this lists the files that are available within the file.
It's a shame it's like that, Android has no trouble either, just seems to be iOS.
Actually, Adobe Reader for both iOS and Android do provide limited Portfolio support. They do not provide the beautiful Flash-based interface that was available with Acrobat XI and earlier, but it does provide a list of the files within the Portfolio from which you can open the individual files within the Portfolio.
Apple's built-in PDF support does not support Portfolios in any way whatsoever other than displaying the default page indication lack of such support.