Severus, I think, wanted the threesome, but is pretending he didn't because it went too far, and Harry had to sort things out. This is what Slytherins do when they lose, pretend it was all a plot or a test or anything that involves them coming out on top.
Harry got Hermione involved to sort out Lucius. She was the one who wrote cock whore on his chest and gave him the rumptying of a lifetime.
Narcissa thought it was a timeturner at first, but when Ron said it wasn't working, she picked up on Hermione's being cross and deduced it was the polyjuice.
She doesn't actually care if she's right. It's just entertaining to get Lucius to think that it's Hermione.