Yes, you can compare them.
But you can compare apples and pears as well.

GS: Bsp / ABT based, Mesh / Model mixture
Unity: Model based without any Scene Management

GS: CAD like editors
Unity: Realtime Editors

Two absolutely different basics. Both not bad. It depends on the project if
you really want to compare them.

Further: You would have to do the same project with both engines, if you want to compare. But that would be no fair comparison, because it depends on the project. For some projects Unity is the way to go, for some projects
you would choose GS, and for another one Unreal.