Better change the permissions for the pathdef.m and classpath.txt files only, or at least only <matlabroot>\toolbox\local. This has a drawback on a multi-user machine: Then all users can adjust pathdef.m to you needs and the next user might be confused.
Prefer user-defined pathdef.m files inside a folder belonging to the user path. This is save and allows individual changes.
I'm using a different strategy: I've edited the <matlabroot>\toolbox\local\pathdef.m to add the folder "D:\MFiles\Inits". This fiolder contains user defined functions to add the personal set of folders to the path dynamically. This allows multiple users to work on one machine and different projects or versions also without the danger of interferences.