For the entity with green eyes, everything made perfect sense.
As a creature capable of dual-gender reproduction most of the time and asexual reproduction when necessary, the Crystal Dragon indeed has the concept of 'parents'.
Although born via asexual reproduction from the Aether Crystal Dragon, theoretically having only a mother, since the mother passed away when it was still a Dragon Egg, Green Pupil spent the vast majority of time with Ian and others after its birth.
And being the first person it saw upon emerging from the eggshell, who taught Green Pupil how to break out of the shell and control its 'other forms'...
In Green Pupil's heart, Ian was undoubtedly akin to a 'father'.
Even the fact that he frequently left home, rarely returning, but always brought back heaps of gifts and taught how to become stronger (Meditation Technique and Essence Furnace Core) - perfectly fit the definition of a father!
