I do not see a master valve/pump or sensor on the Hunter, so not connected to Rachio or enabled in the app. I believe the Hunter’s remote is red, white, & blue. Since Rachio’s remote is your phone, those should not be connected (possibly red & white are, but should not). Everything else looks good from what I can tell.
When I have seen the in-ground irrigation box filling with water, it usually is a valve or line from the main going to the valve (since probably no zones were running). I would let it dry, turn the water back on and try to figure out where the water is coming from.