i'm assuming it's a 4wd car and assuming it's a MT75
in which case, you don't neccesarily need to strip the whole box down to change the VC but if there was anything else wrong with it and he didn't take the box apart and it went bang, he'd be facing a rebuild out of his own pocket, so he's taken it apart to make sure, and it's not a over the top labour charge for the job
mind you, i don't know where you went to get it sorted, but i've had boxes rebuilt for half that and with new bits in but it's mates rates etc so it's not a big deal
the £3k though, thats what you need to be asking yourself about