As you point out, using a constructor on an existing object is something unnatural; I agree that ref($proto) should be avoided in normal cases.
However, there are times when you specifically want to clone or template a new object (e.g. Class::Classless). I you are doing something like this, you should make it clear in the POD that this method call is available, and precisely what it does. This should state (if this is the case) that new can be use both as a class method call and an object method call.
Also, as part of the POD, it forms part of your interface contract. You should write tests which exercise all the options and prove that your code matches what the POD expects to happen.
I'm Not Just Another Perl Hacker
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