FYI - I too ran into zone run times being much shorter than made sense. I use Flex Daily schedules for my lawn and shrub zones. The lawn flex schedule seems reasonable but my flex bushes schedule had way too short of run times for the two zones.
The front zone, which is micro sprayers, was defined as misters and if I put in the real nozzle IPH value the run times would come out way too short, like maybe a minute and about 1-2 time/week. With our old controller we ran this zone twice a day, three times a week. In spring/fall it was running about 2 minutes each time, in summer it got up to 5 minutes each time. With the Rachio this zone seemed to run too short of time but not way too short.
Our back zone is all drip line and it was coming out between 30 seconds and 1 minute for each run time with the correct nozzle IPH which is way too short for dripline. I had to dramatically reduce the IPH to get reasonable run times. With our old controller this ran twice a day, three times per week and for 20 mins spring/fall and up to 60 mins each time in summer.
After reading another post where the answer was to remove the zones from the flex schedule and put them back I did that and the run times went up dramatically and where then too long. I increased the nozzle IPH settings back to the correct values and now the run times now seem reasonable for early Spring - 2 minutes for the front shrubs and 26 minutes for the back shrubs.