I could definitely see why they would close up the outside of TOT early...after all, how many times have you walked right into the hotel with no wait, and go through the whole preamble and finally get to the boiler room and there are about a gazillion people in front of you?! So, there were probably plenty of people who were in line, then riding the "ride" portion after official closing.
We've "shut her down" on the train before too...it's fun to jump on the last train at NOS and then ride around the entire park after closing!