All the settings are from seperate mods, and therefore were not included in Nexgen. But there is a plugin which offers the exact features you are looking for, called
NexgenModConfig. Basically, it can be set up to support any possible .inis, but the modt popular ones are already included in the standard definition file. Read the ReadMe for further information. Whrn I'm back home, i might consider releasing an updated DefinitionFile if there are any requests
Edit: my bad, just realized you only wanna modify which mutators are used. You should be good with boot control, just make sure you enable the tickbox "Enable Nexgen Boot Control" in the same panel.
