GIMP doesn't rotate correctly

Yes, evan_ is correct.

This is a guess, but I would imagine it has to do with the different anti-aliasing algorithms used for preview, versus the actual operation. There are many different anti-aliasing algorithms available. Some are fast, while others can be computationally challenging when working with large amounts of data (pixels).

Because GIMP is designed to work with images of all sizes, those computational costs must be considered for operations like rotation. The "preview" of a rotation needs to occur very quickly, because a user might be rotating an image by hand using a rotation tool. You need redraw speeds that are >30 fps in order for the rotation to appear smooth at all. When you commit to the rotation, GIMP can use a more computationally expensive algorithm. This algorithm will deliver different results when observing at a pixel level.

There are still open questions here, like why is the base layer altered at all? But I suspect that the reasons I've outlined above.