1. 3 story building + mezzanine: Put a roof & perimeter guardrails rails over 50% of that 4th floor deck and call it a mezzanine which does not contribute to either building area or number of stories. This will need to be included/added to fire area and sprinkled.
2. yes, you can install a hatch, req. for any equip. access.
3. You do not count the mezzanine as a story, Design the stairs in compliance with interior exit stairway requirements and eliminate the CPET issue.
...have to keep the occupancy <10 or mezzanine required to be open to floor below.
or just redesign you 3rd floor with a mezzanine and stay off the damn roof!