As you can see in my setup I selected the top edge and applied 2 poly extrusions, first one went along the z axis but the second one went on the y axis.
I get that is somewhat related to edge normals or point normals but why does the base edge suffer changes to that ?

Initially, with your open box, the extruded edge has a normal pointing to +X, so the first extrusion is in that direction. However, that extruded face causes the normal of that edge to be recalculated to +Y, so the second extrusion is made in the +Y direction.

If you picked the leading edge of the original extrusion for the second extrusion (specify it in the group field), it would extrude in the original direction.