Tente
Host apollo hades zeus
Hostname %h.my.university.edu
Se eu estou lendo man ssh_config
corretamente, isso deve fazer o que você quer.
HostName
Specifies the real host name to log into. This can be used to specify nicknames
or abbreviations for hosts. If the hostname contains the character sequence
'%h', then this will be replaced with the host name specified on the command
line (this is useful for manipulating unqualified names). The default is the
name given on the command line. Numeric IP addresses are also permitted (both
on the command line and in HostName specifications).