But a custom template isn't part of the RAW. By creating a custom template you are changing the rules.
It's part of the RAW. By creating a custom template, you remain within the rules and change nothing.
How do you go from the Were-Form template to "oh, I was always only half human"? Looking at the game I don't see adding Changeling, Scion, WCV, or WC Virgin onto a character's existing template. Those are things that you are born and struggle with that heritage, not acquire mid play.
Yup, I was born a WCV Changeling Werewolf Emissary of Power. My childhood was complicated, but now it's awesome. Assuming I have the Refresh to pay for it, what's the problem? My mom was a WCV, and my dad was a Changeling who recently became a sidhe. Later, I figured out the spell to turn into a wolf, and signed on to be a servant of the prehistoric god Urrah, Hunting-Beast-King. My partner is a nephilim (Scion) possessed by seven angry voodoo ghosts who grant him Evocation for the elements of Darkness, Wildness, and Metal (music). We fight crime!
Perfectly RAW, and perfectly in the spirit of the Dresdenverse. It looks funny from the outside, but then again so does Thomas (a sex vampire who pretends to be a gay hairdresser) or Murphy (a tiny kung-fu cheerleader cop hardass) or Harry (a wizard private investigator who can't make any money and is a slave to fairies).
So yes, magical animals are an exception. You could create a custom template that allows weredragons etc but again, we would be departing from the RAW.
Nope, they're specifically allowed by RAW. There's a note about it and everything. You are absolutely allowed to make a weredragon. 100% RAW, and it's literally like three lines under the text you quote. What I find helpful is, when I reference a rule, I read the section the rule is in just to be sure of the context. Doesn't take long, and avoids misunderstandings.