Safe mode prevents malicious or intensive scripts from accessing some of the more in depth features of PHP such as
system() and
passthru(), this ensures that there is a better service for all users and closes some security issues that would be apparent if it were disabled. Although technically part of safe mode, the server can also be set up to limit resources on a server wide basis in the php.ini, as you are describing.
I assume you are looking at the
set_time_limit function and saw the safe mode reference there; basically you cannot alter the time limit on free hosting and even if you could you would be likely to run into problems with resource usage suspensions due to excessive PHP exception times.
On x10premium the limit is raised and on a VPS it can be setup to whatever value you want, including unlimited.