Hi VoCa,
1. Wrapping an App can prevent data leakage; you can configure it to allow or disallow content to be moved outside your wrapped App.
2. App Center offers native viewers for PDF and Office format files, so they can be viewed inside Secure Email only, and not saved externally to the device or accessed by another App.
3. Yes, a jailbreak/root check is part of the default inventory collected. When you first access App Center from your device, you will get an App Center agent that detects this, along with reporting other inventory information to the App Center server. You can treat these "unsecure" devices differently from a normal locked device.