If my border is mostly one piece- and what I'm sewing it to has a lot of small pieces - I put the border on top - that way it easier for me to ease in the "extra" if necessary.
It is easier to control the seam directions if the part with more seams is on top.
If one has a walking foot - it probably does not make a lot of difference, but for me, the part with fewer seams goes on top.