I found the bug. In case when you have SIP fully disabled and you perform the first step of installing TotalFinder's system component (
TotalFinderSIP.osax), there is a dialog which reminds you to disable SIP. This dialog was missing the option for suppression.
This will be fixed in v1.9.1. A workaround for now would be in Terminal.app:
sudo rm -rf /System/Library/ScriptingAdditions/TotalFinderSIP.osax
(Assuming you have still SIP fully disabled) This will delete the system component and return you to situation when TotalFinder will prompt you to install it. That dialog has the suppression option.
Please note that you have to kill TotalFinder.app via Activity Monitor.app and also restart Finder.app via CMD+OPT+ESC, before launching
/Applications/TotalFinder.app to prompt you again.
Hope this helps. I'm sorry for the inconvenience.