Hermione didn't ask why, nor did she argue with him about how if they were to be doing this by the book, the incantation was used for the first transformation. It spoke volumes about the regard she held him in that she did as she was told. The whole process had been doing as she was told, trusting him to guide her since he had the practical experience. If her final few years at Hogwarts had taught her anything, it was that the book didn't always cover everything.
She just stopped with the incantation and focused inward, doing her best to feel it as he suggested. Hermione always had trouble with that sort of thing because it was so far from anything she'd ever really done before and there wasn't a step by step guide on how to do it. If Peter Pettigrew, however, could manage it, she bloody well could too.