If you would still like to use Clean Master, or kill the settings app without any worries, follow these steps.
- Clean flash the build you want, preferably latest.
- When it boots, do not allow the screen to turn off. This is imprtant!
- Go to settings, change all the settings to your preference.
- Once you're done, uncheck "Double tap to wake", if you haven't already.
- Don't close Settings. Reboot from the power menu.
- Done. Screen will not become unresponsive anymore, as long as you do not open the display menu in the settings app. If you do, you will see that the double tap option is disabled. Leave it like that, change the settings you want, then reboot without killing the app.
Bottom line: After doing this, it's perfectly fine if your auto clean app kills Settings, as long as you haven't opened the Display menu.