1. Most likely the bags will be checked all the way to Istanbul. Remember to ask.
2. All passport procedures will take place in Athens. Definitely if everything is on time you will make it. If there are a lot of people at passport control ask the airport people to move you forward because of short time.
3. Something similar happened to me with 2 different bookings, and the first flight wasn't on time, the call center offered me to book me to the next Istanbul flight. ( I declined because there was a TK flight before the A3 one, I booked this myself, and at the end the customer service paid me the difference of the two tickets).