I think this has to do with the additional geometry. If you have the lower cube geometry in Model2, blender sees the extrude in the upper face as an extension and only extrudes the actual face. Model1 is standalone BUT I don’t know either 🙂
What I do know is that if you select CTRL+E and Extrude Edges or simply select Edge Mode -> select Edges and then E, you can work around this. You just have to know how to help yourself
