There is a big difference between keeping file in /tmp and keeping files 
in /home/jsmith/research/tmp.  I would think that a reasonable user 
would expect that when they are told that their home directory is backed 
up that includes /home/jsmith/research/tmp as well as 
/home/jsmith/research/core/ which might mean the "core" research.

You can however disagree and hope you never have to explain to your 
management why they were foolish to use that name you never warned them 
about:-)

David