I have answers to two of these questions:
First of all, your objects are not hidden from TMSH, they are in a subfolder for the iApp Service that you have deployed. You can see them in TMSH if use the recursive keyword on your list commands or is you list the contents of the folder by name.
Second, the reason why you cannot edit the objects created by the iApp outside of the iApp is a feature called Strict Updates. This feature allows the iApp Service to protect the objects that it created. If you need to override this behavior, you can turn off strictness.
Here is how to do that:
1) Navigate to iApp -> Application Services
2) Select the iApp Service that you have deployed
3) Click on the Properties tab
4) Toggle the Basic/Advanced Application Service drop-down value to Advanced
5) Clear the Strict Updates checkbox and click Update
Now you will be able to edit the objects outside of the iApp. Be warned that if you reenter the template at some point in the future, you may end up overwriting any changes that you made outside of the template.
Anyway, I hope that helps.