I was wondering about that too... According to the spec:
/home is a fairly standard concept, but it is clearly a site-specific filesystem. The setup will differ from host to host. Therefore, no program should assume any specific location for a home directory, rather it should query for it.
Sometimes home directories are in other locations. My University used to have different mount points for different graduating classes on our Unix servers. And I use "/home2" for one of my servers for... reasons.
Though I'm not sure that qualifies as "deprecated"? I get the "non-standard" bit though.
You also have to consider that roots homedir is in /root and not home, so if you'd just assume it's /home/$USER you'd get in trouble when your programm is run or compiled as root.
In the user's home directory, which may or may not be in /home/username.
grep username /etc/passwd will show you the home directory for a user. Also ~username from the CLI will resolve to that user's home directory. e.g. cp file.txt ~username/Documents/
My best guess is that having programs treat a user's home directly as a location for things like config files is deprecated. Programs should be following the XDG standard instead.
You could contact the author (their email address is in the image), but I'm too lazy to do that.
The legend seems confusing to me. I think it's trying to say that /home is non-standard. Notice that the description for /var/run explicitly states it's deprecated, and has a solid border.