Basically I was trying to figure out if there's any advantage to operate a via flight over two separate flights. Are there any differences between the following two scenarios assuming both planes depart CTS and HND at the same time?
AA123 CTS to OKA via HND
AA123 CTS to HND and AA125 HND to OKA operated by the same aircraft
The only advantage I know of is that through the Via flights, you could possibility shorten your transfer time while the first flight lands in HND. For example, HND has min. transfer time of 1.5 hour. However, if you use something like a B737 or A320, you could technically take off for OKA after 1 hour on the ground (airplane's turnaround time), thus saving you 30 minutes on the trip. If you are fighting for connecting passengers, sometimes 30 minutes makes the difference in the ORS. But for all your other connecting passengers from other flights who wish to get on the HND-OKA flight, they have to follow the min. transfer time.
When passengers continue on the same aircraft, the minimum transfer time does not matter. This applies in general, not only for via flights. There is no difference between a via flight or two independent flights except for flights in Africa under the Yamoussoukro Decision.