I would always presume that given a choice of doing what is in its own self interest verses in the customer's interest, a bank will ALWAYS do the former rather than the latter.
Banks are in the business of making money, always presume that their policies, processes and contractual terms will be slanted to maximize their ability to make money. It's not being evil or anything, it's just business, they are under no obligation to be altruistic or do what's best for you at the expense of their profits.
So, especially since it's not exactly a hardship, I would always make extra principleprincipal payments using a separate check and clearly mark it as an extra principleprincipal payment.