For me the problem with putting the intermediate stop in the window is that it requires the pilot to remember to reset the altitude once the intermediate stop is passed - and pilots are fallible - VNAV is pretty damn reliable and will fly the profile pretty much automatically.
A failure to resume climb after the intermediate stop is just as much as bust as is a climb through an altitiude.
NB I think the question is relevant to recent products from Boeing/Airbus, cos older types can put you in funny unexpected modes, (by knocking the pitch switch or changing pitch modes close to the level off, for example).