Many universities just toss you an MS degree along the way for free in your PhD, but coming in with one has no real effect on your PhD length besides waving some clad requirements. At the end of the day US PhD programs just assume you will do 5 or more years of research, for those looking to be professors this is a boon as many US PhDs skip the postdoc step often required for EU PhDs which are typically 3ish years.