Documentation states:
When called, set_time_limit() restarts the timeout counter from zero. In other words, if the timeout is the default 30 seconds, and 25 seconds into script execution a call such as set_time_limit(20) is made, the script will run for a total of 45 seconds before timing out.
If I have a long running script and i want a exact time limit, I set this as near as possible to the first line.