Firstly, I don't understand why you want to disable rootless!!! Only developers in mac os team will require it. Esp. when they're trying out new kernel mods or drivers. A normal user doesn't have to care about it at all!!!
Both TotalFinder and TotalSpaces2 work by injecting code into processes that are part of OSX. They change the way those processes work, but they don't change the underlying system - they just add features whilst they are running. If you quit TotalFinder or TotalSpaces2, those processes restart and system returns to its original state.
However, in El Capitan OSX 10.11, this kind of modification will be disallowed by a new feature called "System Integrity Protection". It is also known as "Rootless". The feature prevents both modifications to your system files, and to system processes whilst they are running (even if you enter your password for administrator access).
So in a normally configured Mac, TotalFinder and TotalSpaces2 cannot run.