We've gotten the letter, too. My son was out 2 weeks to visit his grandmother in a different country. We told the school months ahead of time, and they were completely fine with it, but warned us that he would get a truancy letter because the letter was mandated by the state. As there were absolutely no consequences tied to the letter (for us at least - I'm not clear on whether it affected the school's funding) , we were fine with it. I was surprised when the letter came directly from the school principal and not the state, but I guess it makes sense that the individual schools are responsible for fulfilling a state mandate on attendance matters.
Talk to the school again. It is very possible that the letter they sent was mandated, and that what they told you in person is how the school really handles attendance matters.