This Flex Daily FAQ talks about the watering duration:
http://support.rachio.com/article/382-flex-schedule-faq
I noticed that they talk about managed allowed depletion (MAD) changing the duration, so that would be my guess as to why the ‘inches of water’ changes.
You might play with it to see if that’s indeed the case. Note that changing MAD can be a bit tricky and end up changing both duration and frequency, whereas crop coefficient only changes frequency and the nozzle precipitation rate only changes watering duration. I think most people keep MAD at 50%?