I'd recommend reading this article which explains everything fairly well: Coordinate System
As the article explains, each graphics item maintains it's own coordinate system. The methods you are referring to are used to translate coordinates between those items, between the items and the scene and so on.
I hope that reading that article will help, otherwise feel free to ask if clarification is needed.
After further investigation, it appears that this is because I am using OpenGL - the 'fullUpdate' flag in updateScene is always set in this case - qgraphicsView has "accelerateScrolling = !isGlWidget" [in setupViewport, line 2759] and "fullUpdate = !d->accelerateScrolling" [in updateScene, line 2675]