You are talking about NEC like it has detailed code for low voltage wiring. It does not. Most of the code it does have is about how to run the low voltage wire through the fire barriers as well as older analog telephone & alarm wiring.
I respect your desire to be cautious and agree that if there is a way to configure the zone wiring in such a way that two controllers could act independent of each other it is perhaps the “best” solution (if you don’t count effort required), but using isolation on commons has it’s own set of issues, such as controllers not being able to water at the same time (if schedule happens to coincide):
I’ve been dealing with controller interconnects for a while on these forums, I’ve yet to get any feedback that something went wrong after commons where interconnected.