Here we see already an automatic feature of Mathematica: It allways tries to scale the SurfaceGraphics bounding box to x : y : z = 1 : 1 : 0.4 and cuts all z values, which exceed the z bounds of this box. JavaView does not scale the coordinate axes different and does not support such an automatic clipping.
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ClipFill is an option for SurfaceGraphics that specifies how clipped parts of the surface are to be drawn. In[1]:= cf = SurfaceGraphics[Table[Sin[x]*Exp[y], {x, -Pi, Pi, Pi/4.}, {y, -E, E, E/4.}], ClipFill -> {GrayLevel[0.], GrayLevel[1.]}];

In[2]:= JavaView[cf]

The ClipFill option allows to mark or not draw the clipped faces - as JavaView does not support the clipping, this option does not work in JavaView.
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