If the app is hard coded it shouldn't trust another cert. Note though that browsers, like Chrome, ignore cert pinning if the cert chains up to a locally trusted CA. So the answer is more "It Depends".

> Chrome does not perform pin validation when the certificate chain chains up to a private trust anchor. A key result of this policy is that private trust anchors can be used to proxy (or MITM) connections, even to pinned sites. “Data loss prevention” appliances, firewalls, content filters, and malware can use this feature to defeat the protections of key pinning.

http://www.chromium.org/Home/chromium-security/security-faq#...

EDIT: Spaced on the fact this is a phone app. While Chrome on Windows ignores certificate pins, I'm unsure if this also applies to Android / iOS root stores as well.