When creating a matrix project with 2 or more axes, the axes can be dragged and dropped to change the order. But unfortunately that has no effect. The axis order seems to be defined by the length of the axes.
The attached screenshot illustrates that.
The axis with more values seems to be always the y-axis.

The problem is that using the matrix sorter plugin does not really help to sort the executions. The plugin allows to sort execution by the last axis. But that does not work properly, if the last axis cannot be defined.