Is there any way to add a float valve? You can present water to the valve (say once a day for 15 minutes) and water would only flow if the water level dropped to a point to open the valve. You would need to regulate the pressure to within the valve's specs (usually less then 30 psi) and you would need a flow sensor if you wanted an accurate estimate of the amount of water used.
Note: You couldn't rely on Rachio's built in flow estimate since it assumes water is flowing the whole time the solenoid is open.
This way you are not wasting water, nor having to estimate evaporation loss and trying create custom nozzles and schedules to refill the correct amount.
This is how I setup the autofill for my pond, except I am running the water through a homemade activated carbon filter to remove the chlorine first. I don't think you'll need this step unless you need to add chlorine to maintain the pool's chlorine levels.
You could also add a rain sensor to stop a schedule from running if it is or did rain recently.