Shapeshifter doesn't change everything. I haven't used it but would imagine it changes standard widgets(scrollbars, table headers, aqua buttons etc etc), not custom ones.
prove me wrong.
This is yet to be seen by me... Ah well my new mac is coming next week and I'll install shapeshifter on it and have a play. I would think that having widgets that don't at least take on the look and feel by inheritance (they can still look different) would be a major development mistake... Even Microsoft do this.