Running the following code emits the same warnings for all the three usages of isa. I'd expect something else when reading "This can generate many extra warnings, but they're more specific as to the actual wrong practice and they usually suggest proper fixes" in the documentation.
#!/usr/bin/perl
use warnings;
use strict;
use UNIVERSAL::isa 'verbose';
my $x = bless {}, 'MyClass';
warn "$] $UNIVERSAL::isa::VERSION\n";
warn $x->isa('MyClass');
warn $x->UNIVERSAL::isa('MyClass');
warn UNIVERSAL::isa($x, 'MyClass');
Output on my machine:
5.018002 1.20150614
Called UNIVERSAL::isa() as a function, not a method at ./2.pl line 10.
1 at ./2.pl line 10.
Called UNIVERSAL::isa() as a function, not a method at ./2.pl line 11.
1 at ./2.pl line 11.
Called UNIVERSAL::isa() as a function, not a method at ./2.pl line 12.
1 at ./2.pl line 12.
Same with Perl 5.25.7.