here are answers
1. Title field 1 and 2 appear in look up and on form top bar .
2 & 3. Both used fir security purpose. config key to enable /disable functionality . Security key to enable disable access to particular object
For all indexes
msdn.microsoft.com/.../hh812105.aspx
For formref
community.dynamics.com/.../formref-and-go-to-the-main-table-form
All of these can be created and changed in AOT