Mike,
There is not a code requirement thatI know of. Although most of us will install them in sequence.
Based on what you have said you have a moral reason to ask the contractor to change the switching sequence.
Other than that,its his prerogative where he wants to charge for this service.
Mike don't look at this in a negative way.It will give you a opportunity to meet the contractor ( if you havn't already) and ask all kinds of questions and get a insight of how your home is wired.
Wayne