My understanding is that Gwyndolin was born biologically male, but under the moon and with magical affinity, both of which are associated with feminity for the gods which lead them to raise him as a daughter like you said. So I think he's cis but raised in that stereotypically western fantasy feminine style.

Of course it's hard to tell, given the opaque nature of DS lore and which translation you're referring to (see: Throne Watcher in DS2 having differently gendered pronouns across different languages)