Perhaps it is a good thing. Sora's wording brings Vanitas up short. He had been about to laugh, expecting some sort of answer about being friends and helping Vanitas realize the power of having a good friend. Instead what he gets is about acceptance. The thing is that right now that's probably all Vanitas can ask for.

"I doubt Ventus understands any more than you do," is what he says. Partially because Vanitas has a hard time wrapping his head around it. Sure people say that they want to understand all the time, but that's usually because they want to change you. It's not usually because it'll help them accept you.