If it is the system-wide vimrc, this option won’t be off. So, if you’re changing the system-wide vimrc and you want it, you need to set it.
From the documentation section *compatible-default* (emphasis mine):
When Vim starts, the ‘compatible’
option is on. This will be used when
Vim starts its initializations. But
as soon as a user vimrc file is found,
or a vimrc file in the current
directory, or the “VIMINIT”
environment variable is set, it will
be set to ‘nocompatible’.
Another difference is that explicitly setting ‘nocompatible’ overrules calling vim with the -C flag.
In any other scenario, yes, setting ‘nocompatible’ in your vimrc is a noop.
In the end I think it’s just a matter of “better safe than sorry”.