Maybe this issue is tied to SolidWorks inability to handle ZTG.....maybe it is a setting in regards to how SolidWorks calculates area when dealing with surfaces that touch.
Well, in reality, since those two are mated, the surface area really hasn't changed. Those two surfaces haven't been "absorbed" they are still there. What you are looking for is the external surface area of the assembly.
The only way that I know of is to select all the visible surfaces and then use your measure tool.
I do understand that there might be too many to select in some assemblies, so failing that, there is this method:
And then there is this macro:
Although I cannot speak for the accuracy\ validity\safety of the macro.
I never used it, I just did a Google search.