Are any of these zones also spraying in the front yard? Hopefully not…
What you can do is set all the zone parameters for these zones in the backyard to exactly the same values. That way they will always water on the exact same days. Obviously there is some inefficiencies here as if one of the zones is in full sun and another shady, one zone will be watering too much. But I think this is a reasonable compromise for your situation.
I would place a bunch of catch cups or tuna cans, etc. all over the backyard and run it zone by zone and collect the numbers. This way you know how much water from each zone is going where (in case you want to try modifying nozzles or changing sprinklers for better coverage later - you’ll need this info). Then you can add up all those numbers together for your total precip rates in that catch cup for all the zones. Do the catch cup efficiency math on these totals and put them into Rachio (for every zone). Now all those zones will have the exact same settings. Not idea, but with such spread out sprinklers overlapping multiple zones, it’s a decent compromise.