I was holding off answering because I read something on RIM's site that answered your question. Alas I haven't been able to re-locate it yet.
The question can be thought of as a macro for some of the other permission questions. If the user answers negative, then any subsequent access to an API that needs user permission will cause the normal prompt. Answering affirmative will allow a subset of common permissions. If I remember correctly these include access to location and PIM data and access to the network. It is different from the programing API signing key issue. An application signed for access to PIM data will still need user permission to access the data, unless installed from the BES with appropriate permission.
Regardless of the original answer, the user can change permissions later by editing application and/or module permissions.
Found it! This video talks about Security Prompts.
Trusted applications are available from OS 4.5 and have all permission set to ALLOW except those that are set to DENY by default.