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There are 2 kinds of bounding box -- visual (default) and geometric (which I think probably should be the default). The visual bounding box includes the stroke width in calculating the size of an object. The geometric bounding box ignores the stroke, in calculating the size.
The geometric bounding box would be the same as the middle of the stroke, since the stroke is placed symmetrically on the path.
Inkscape Preferences > Tools > Geometric bounding box.
So I don't have to re-read the whole tutorial, about where in the tutorial is the part about setting the point of reference? I think using the right bounding box will solve your problem, but I'm not sure. I need to remind myself about the point of reference.