In the example select one of the squares and see how the scene rect is extended to include the untransformed bounding rect of the square.

I'm pretty sure the following line is the culprit, or the fact that ensureSceneTransform() isn't called:
https://qt.gitorious.org/qt/qt/source/68a911862e05400ced87971c43fb27fb5d5d8ebd:src/gui/graphicsview/qgraphicsscene.cpp#L5200