The mixing of zones is the number one problem in legacy irrigation systems (in my opinion), particularly drip systems. I wish someone had educated me on this many years ago. Root depth is king. You simply cant mix a plant with 4 inch roots with one with 24 inch roots on the same controller valve and get good results. It is as simple as that. If and when i lay out my yards again, i will run two lines to all major locations (except grass). One will be for short and one for long (trees) roots. I will even move young trees from short to long after a few months of growing, which will be easy if the pipe is right there already.
At the end of the day, until you adopt a two valve system, you have to water to the most sensitive plant, the 4" root, which will eventually kill the tree due to saturated soil and low depth roots. You can improve the situation if you turn off watering to the trees during all but the summer growing season, and instead water it monthly by hand, but keep an eye on it. Most plants require an inch of water per week in the peak growing season to the root zone, so that might help with your calculations.