The height markers at IOA and USF are VERY accurate. An actual height line to measure your child is located in numerous places including: Outside the entrance to the park, at each Express kiosk, at the entrance to each attraction, and on the loading platform of each attraction. In addition, many times the attendants on the load platform will measure your childs height if they believe they may not make the height requirement.
Yes, all the height measurement tools are VERY accurate. No, Disney doesn't add an inch "just to be on the safe side." In fact, you'll notice most of Disney's height requirements are much lower than Universal's (compare Kali to Bluto's) - kinda makes you wonder who adds an inch "just to be on the safe side!