ssh assumes /home/$USER beeing the home directory and looks for keys and known_host under /home/$USER/.ssh! In my opinion it should try to read the $HOME variable and only after that start guessing.
All the tools use the home directory specified in the user's passwd file entry, they certainly don't "guess". I don't think that this will change.
Change all RESOLVED bug to CLOSED with the exception of the ones fixed post-4.4.