Really depends on the user requirements. What I see with novice users is that the standard menus of Mail.app are already scaring them. I assume 90%+ of the people in my company do not know what mail headers are, what encoding is, or why IMAP accounts work different from POP, what the difference between a signature and signing a message is, why attachments work differently on Windows etc. Adding a lot of functions which only a fraction of the users will ever need comes at a cost. If I imagine the task of explaining to my mother (89 and using Mail.app without problems) what all the different options in the MailTags window are for (which I would have to do, if they were there), I prefer this to be an add-on myself. Especially since some of these third-party add-ons offer integration options (e.g. with DropBox or OmniFocus) that Apple would never offer (their support of Twitter or Facebook as sharing options does zip for me).
But, of course, this is a matter of opinion. I just think it is absolutely workable.
I think you've captured it. To pile on a little more, adding more features that perhaps 1% of users will use incurs UI cruft, additional code that could cause bugs in other more commonly used pieces, and costs development time that could be invested in a feature (for anything else) that far more users will take advantage of. This is all ignoring that if Apple were to listen to all the various 1%'s to satisfy their little bugaboos (that can be solved with third party tools or scripts) would constitute design by committee, which is pretty sure to turn out a monstrosity.