Could you add in your surname to the mix? Maybe so that it reads:
FirstName UnusualSurname NewSurname (William LoserDad DucksNuts)
Or perhaps:
FirstName NewSurname UnusualSurname (William DucksNuts LoserDad)
I don't care for the look of hyphenated names, but that could work as well if you don't mind them. They could go by both last names (how proper!) or simply by whichever name you choose as the
last last name.
I think it would be an appropriate way to nod at your guardianship and maternial biological ties, whilst still being respectful of their paternal biological ties (and allowing them the benefit of choosing for themselves later in life whether to keep their father's last name or change it). I would think it may make it easier a leap downline, too, for them to assume your own surname if it has spent a lifetime being incorporated into their identity already. It seems more positive an action, too, which seems to fall in line with how you are choosing to handle the situation