The highlighting stroke has always been on top. If you use a highlighter color that's transparent, then it will take a huge number of strokes to eventually block the text it highlights, thus giving the appearance that the highlighting is behind the text. But if you try using a highlighter color that's more opaque, it will take just a few strokes to eventually cover the text. That means highlighting strokes are always on the top layer.
On dark paper, the general brightness of the paper is now detected and the existing strokes are adjusted accordingly to increase their visibility. (Previously, if you drew or highlighted a white stroke on dark paper, the stroke would be almost invisible.)
Technically speaking for light papers, a highlighting stroke blends with the text rather than goes behind it. It just looks like "behind the text" for the blended effect. For dark papers, due to the limitations of Apple's blend mode, the behaviour on the dark paper is currently the best we have implemented so far.