I thought it was the fact that it was the 'duplicate' Borden that tied the knot, thereby meaning that everyone was unaware of the knot used. This was alluded to in the funeral scene where Angier asks Borden what type of knot he used, to which he replied he didn't know. This would make sense if the dupe had tied it, the other Borden wouldn't have had prior knowledge of which knot was used, or not!
If you watch it again everything starts to fall into place a bit more. I love this film.