I do not disagree with the considerations you make, but I think that greater emphasis should be placed on the most important disadvantage, namely that doing your Master's somewhere and PhD somewhere else almost invariably extends the overall duration of your graduate studies. If one does not know ahead of time whether or not one will be interested in going for a PhD, doing a Master's degree first is very sensible idea, but staying at the same school for the PhD means (aside from your correct remark about not having to retake courses), that one can spend more time working on the project that will eventually lead to the PhD itself.
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Massimo
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