Thanks for the feedback, Geertjan.
Roughly said, the Model-Mode moves points, the Object-Mode changes the axis. (Yes, Model Mode has options to change the Axis positions for example, there the confusion starts) For animation the Axis information can be stored in Keyframes without (!) destroying the point values. In this way the point values stay relatively the same and the XYZ numbers are the same after scaling. In some cases the Model Mode on the other hand, could lead to scale the object in a way that all points are zero. This would be the end, as from there—no scaling would bring it back. (1000 times zero equals zero)
Model Mode is great for preparation, but in terms of scaling a Primitive Cube not really useful.
Again, roughly said. It has as well other reasons, to not distort the axis relations, but that is of course another theme, for modeling, I gave you the hint already. For animations this difference is a “must to know” information.
My best wishes
Sassi