Hello Jason,
When a new version of MATLAB is installed, it will not try to get the old "pathdef" file out of the old version of MATLAB. What may have happened is that you have a "pathdef" file in your "userpath" directory. If there is another "pathdef" file that shadows the default file, then the other file will be used.
This is not the recommended practice. It is far safer to only have one "pathdef" file per installation, which contains only the default path that was installed with MATLAB. This is usually located in (matlabroot)/toolbox/local/.
Any user-defined directories may be added more safely from within a "startup" file, in the way you showed above. This is what I believe is the recommended practice. The difference between having the user-defined files in "startup" versus in "pathdef" should be nearly negligible in regards to MATLAB startup time, so don't worry about slowing everything down.
I hope this helps!
-Cam