Yes, the default UNIVERSAL:: methods don't do what the overriding methods do.
The guide you refer to prefers UNIVERSAL::isa (etc.) over $obj->isa because
$foo->method croaks when $foo is a reference that isn't an object. This has
the cost of breaking anything that overrides the UNIVERSAL method.
I've started preferring always using the method call, wrapped in eval:
if (eval { $obj->isa("Foo") }) {
print "It's a foo!";
}
The only drawback that I see with this so far is that $@ is altered and would need to be localized if it's being otherwise used, such as in a DESTROY routine.
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