Manila to China flight then to Japan

Hi, I wish to vist PRC for the 72 hours. Unfortunately I can't find any flights from Manila to Japan via PRC that suit me.

Is it possible to book a single flight from Manila to PRC. Then book another flight from PRC to Japan that would leave within the 72 hours.

I'm a bit confused as to does the visa only apply if you have a layover. Or can you have two separate flights, just as long as they are booked beforehand and within the 72 hours?

Thanks