The 2 cycles are still used in the same session.
Meaning it will water zone 1, then zone 2, then could pause to let water soak, then do a second cycle of zone 1 and then zone 2. If there is a third zone, the pause would be shorter (on non-existent): 1-2-3-rest-1-2-3 [2 cycles]
I guess it is possible if you have a lot of zones with certain setups (soil, plants) with extremely long water times that a watering of all 12 zones could run into 10 am, but unlikely.
Rachio won't water zone 1 a bit, take a nap, then come back later in the afternoon to do zone 2.