By definition, both solutions are supposed to run the motors the same length of time if motors are running the same RPM. Generally the single larger battery is a little lighter and so it will need less power to fly and so it will fly a few percent longer. To run batteries in parallel you must be careful that they are charged to the same voltage before you connect them together.
For flight duration time, it's more important to select lower RPM with larger prop which is more efficient that higher RPM with smaller prop. Be aware that RPM increases if you increase cell count and RPM also increases if you increase KV, and for instance doubling either one will double the RPM. Large props with low pitch are not capable of flying fast though, so there is a trade off to more medium sized props if your goal is actually distance and not just time.
2 blade props are more efficient than 3 or more blade props.
A switching BEC to power FC, receiver, etc. uses less power than linear BEC.
A fixed wing airplane will fly much longer and much farther than a copter. It is easy to build a fixed wing (electric or internal combustion) that can fly for an hour or more. It is difficult and expensive to build an electric any-copter that can fly for an hour.