The scanner preference scanner_plugins_timeout doesn’t set the overall scan timeout. It is for plugins which belongs to the ACT_SCANNER category.
The scan duration depends on many factors, like amount of host in the target, if it includes the UDP ports, but also depends on the target. If there is a firewall in front of the target closing the ports detected as open, each plugin will run until it timeouts.
There are some option which can speed up the scan in case a port has been closed during the scan, like open_sock_max_attempts