Hi,
that depends on the Management Pack version. TimeoutSeconds used to be overrideable in version 6.0.6667.0 but it isn't in 6.0.6989.0
You can easily check this out by going, in the Ops Console, to Authoring\Monitors. Search for "Logical Disk Free Space" for Windows Server 20XX, right-click, create override etc. etc. and then check if the TimeoutSeconds is present as an overrideable
parameter.
However, if this script times out - there's some serious issues with the servers itself and as you mentioned already it's overloaded.
In these cases I tell the server owner that SCOM can't run properly on his server unless he fixes the performance issues.