With Mathematica 10.4.1 on Windows 7 x64 I get FrontEnd crash with your code by default but switching to "Graphics3DRenderingEngine" -> "BSPTree" produces the expected output whish is relatively responsible (comparing to the Image3D):
SeedRandom[10] i3d = 1/4 RandomReal[1, {5, 5, 5}] // Image3D 
Style[Show[{i3d, Graphics3D[{FaceForm[Opacity[.6]], Cuboid[{3, 3, 3}]}]}], RenderingOptions -> {"Graphics3DRenderingEngine" -> "BSPTree"}] 
The option RenderingOptions -> {"Graphics3DRenderingEngine" -> "Software"} produces the same but seems to be even slower.
An attempt to Export this as PNG with ImageSize -> {2400, 1600} crashed my video driver and I got not responding FrontEnd taking 100% CPU time of one of my cores.