If anyone is interested - the final value of getUsedCpu is about 0.8 ms less than the final one shown on the web page.

You can e.g. use this information to manually keep track of where your CPU bucket should be (http://support.screeps.com/hc/en-us/articles/204332302-Understanding-CPU-limit-usage)

I'm guessing the extra CPU time is due to the game finishing up some stuff after the game loop.