Most of these settings define what happens at compile time. Because of that you can only read them at runtime, but not change them. For example, the LinkIn settings define which information is added to your EXE file at compile time. And the active error search options require the use of a custom memory manager, so turning these options on/off on the fly doesn't really work.
You can change the CheckForFreeze stuff, though. There are APIs available for that, see "PauseFreezeCheck()", "ImNotFrozen()" and "SetFreezeTimeout()".
My recommendation to you would be to link in some reasonable default settings into the EXE file, but then to change everything that makes sense at runtime.