The ATLAS does allow for both DNIS and/or ANI "manipulation", in both the NETWORK TERM and USER TERM of the DIAL PLAN. This substitution takes place on the egress interface, not ingress.
So under the DIAL PLAN and either NETWORK or USER TERM, just past the IFCE CONFIG is SUBSTITUTION TEMPLATE. If you don't want to make any change to the DNIS, you should put "$" as both the "DNIS Orig #" and the "DNIS Subst #" then go into the "ANI Subs".
In here you can put the "ANI Orig #" as "XXXX" and the "ANI Subst #" with the desired Area Code and Exchange (i.e. "256-963-XXXX")
Hope this answers your question,