Submit a feedback on the TK website in order for the upgrade to include both segments; otherwise it will only be IST-ATL as shown to you currently.
No it will not become cheaper. 45k miles is the normal/standard.
In theory you could book a new I class ticket TBS-IST-ATL for 45k miles + tax (and you can refund the X class ticket you have now). Try searching for award availability from TBS to ATL for your travel date.