To answer your question - yes the email is configurable. Either through property over-rides or spring over-ride. If needed you can plug in your own implementation.
I've not seen that text in the documentation before, but it seems incomplete to me. In particular why should your instance of alfresco be sending out anything from alfresco.com, that may be a default value somewhere but it is not correct.
I think you may be misunderstanding what mail.from.default does, it is the address used when there's nothing else available. That's not always what's wanted especially if there's a very strict email server on the other end so there's an option in 4.0.1 to force the email system to use the the default address, and never use anything else. You could pick that up from HEAD and patch it if that's what you need.
