I have been thinking alot about this problem. My problem is slightly different that yours But I think the solution might be the same for both. Mine is where the crop ET for the day ends up being more than the irrigation amount scheduled to be put down that day. I know that some folks have either manually added water later in the day, or set up a "temporary" fixed schedule to take care of the problem. For one zone (of just flowers), I tried making the root depth a little deeper to get it to water longer just for those ET>watering days.
I would really like to see if there could be a more automated process as well -- I travel, often to places where I only have access to wifi once a day, if that. So I REALLY need automation. And right now, when I add the second watering myself, I've just been topping it off a bit (drip zone had run in the morning for 67 minutes, I add 20 minutes late in the afternoon) -- I've been doing some reading, can't find the exact answer, but my gut is saying that I really should run the whole 67 minutes again to make sure the water gets down deep enough.
And Rachio is going to have the issue of how often the weather station is sending data, as @plainsane said. In my case, I see changes to my moisture level data throughout the day, and the system deciding that it needed to water after all, so it is obviously checking more than once a day.
It would really be nice if we could choose by schedule whether to let it check and run again in the same day. In my particular case I would not want/need the lawn to function that way, but I sure as heck would love to have my drip zones work that way!!! And I'm sure there are plenty of people out there who would want it for their lawns.
And yes, I love my Rachio, and I love even more that the Rachio team monitors our forums and values our feedback.