anyone know why knife cut don’t produce a clean mesh. rather, see the red circles in the picture, why do those lines remain when you knife cut a shape into the cube
Because it would be impossible to define that as a polygon without a bridge between the outside and inside loops, and still have a connection to the inside face.
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Not impossible… some 3D apps can do this… but the internal representaion structure of 3D data used by blender simply doesn’t allow this. It’s more complex to do it and usually not needed in a polygon modeler. So it’s an software architecural design question.
(Useing 2D curves you can do something like this… using fill mode…)
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The use of the name polygons is not restricted to “ordinary” polygons…
Also Maya seems to be able to do this at least since 2014:
docs maya 2014 Editing_polygons_Make_a_hole_in_a_polygon_face
Someone may also follow on this page → Create a polygon face with a hole
The implemantation may even use internal edges for this… but at least doesn’t show them…
Anyway:
This all starts with the assumption of the OP to have “a clean mesh”… nothing has to be “clean” whatever this means if you can’t see it in the final render 
And:
Someone might also consider this as “clean”:
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This is because Polygon requires at least three Vertex connections to create Face.
For SketchUp, as asked, you can cut the polygon cleanly.
But that’s what the software shows. (Hidden) 
Yes, 3dsMax can do it too, it only needs a single edge to connect N-gon faces to adjacent.
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