It doesn’t work like it should. What seems to happen is the X and Y axis of the fueling tables are used correctly but then the changes are applied to all values of the Z axis. I was able to work around this by just tuning one Z value at a time but that won’t apply equally to all users.
(in my case I have a 3 stage intake manifold, and each stage is a different Z value).
You are correct, support for the Z axis is not implemented in the VE auto-tune.
It would be relatively straightforward for a case like yours, where you have three distinct positions on the Z-axis. However, it becomes very complicated when you have a fully variable Z-axis, allowing you to be positioned between Z slices, and the Z-axis changes during the run.
My current idea is that we could add an option to manually select which Z slice of the table should be modified by the auto-tune.