Both "mapred" and "hdfs" users have the same home dir.
A user reported having some problems with their config management system overwriting the "mapred" user permissions of the PID directory (Which is also its homedir) with those of the "hdfs" user (Same homedir as "mapred" user), which causes the tasktracker process to fail to start, since it now cannot write to the PID dir.
Although the config system can be fixed not to do that, if both users had separate home dirs, this would not have been a problem, and the separation would have only been logical.
I think after the username separation Hadoop has had in packaging terms, the homedir split does make sense.
Its just 1/0.22 versions of Hadoop and their packages that could be affected by this.
Presently, for 0.23+, I think we have /var/run/hadoop/ for all things HDFS (Should we rename?) and /var/run/yarn/ for all things MapReduce2 which makes sense and should be good enough.