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!";
   }
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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.