You can use them, but it is hard for us to troubleshoot when people say "My phone just rebooted, why?" with no other information provided
I created the settings in tools to be very specific to this kernel and rom and believe them to work best. That is why we suggest using what is provided.
So far talking with someone else using the rom Go Power Manager looks like it may be a culprit for random reboots. That is not a definite but a very strong maybe. So as this is a brand new release we need help troubleshooting issues. One of them is to ask people not to restore a bunch of stuff or use a bunch of CPU and system tweaks. Hard to troubleshoot other people's apps etc. It is a lot easier to start with what we create and fix the problems internally.
Thanks and enjoy the ride!