Your two ways of testing undef don't actually do the same thing.
if defined $var
will execute your statement if $var is defined. unless $var eq undef
will execute your statement if $var is undef, the empty string, or something else that will stringify to the empty string. Try the following code snippet to see for yourself:
my $var = undef;
print "Undefined!\n" if $var eq undef;
$var = '';
print "Undefined again!\n" if $var eq undef;
This happens because the "eq" operator stringifies both of its arguments, and undef stringifies to the empty string.
The warning doesn't exist just to critique your syntax... it's warning you of a danger that your code might not be doing exactly what you think it is.