You can send your documents to other apps using an UIDocumentInteractionController object. You initialize it with a file URL pointing to your document and then use one of it’s methods to present it.
This takes care of displaying a preview (if possible) and letting the user select the application the document should be opened in.
The document has to be decrypted for this to work. You then cannot make any guarantees about the security of your file - once it is handed over to another application it is out of your control.
If your app doesn’t explicitly opt-in to use iCloud sync your data will not be synced with iCloud. What will be sent to iCloud are backups of the whole device though (if enabled). There are ways to disable this for single files as you already read in the question you linked.
The iOS file protection is based on a device key, not on a per app key. This also is not necessary because apps are protected from each other by the sandbox, unless your phone is jailbroken. On a jailbroken phone there are no security guarantees.