So, once I finished the game, I started digging around inside its files. (On a Mac, you can do this by right-clicking the app, and selecting "Show Package Contents".) Among other things, you can learn that the son of Naija and Li is named Lucien, and the female character that looks similar to Naija, seen sleeping in Naija's home in the (second) ending sequence, is Lucien's girlfriend (her graphics are filed under "luciengf").
A few interesting things I found...
First, the ghost boy in the sunken city is referred to as "CC". His graphics and scripts are filed under "cc", and there's a "cc_cat", "cc_father", "cc_mother", etc, all of which are used in the city. (Apparently the woman who likes flowers is "cc_gf" -- CC's girlfriend? He seemed a bit young for that, but I guess I had crushes on girls in elementary school.

) I'm not sure if that stands for "creator child", or "city child", or if it's really a name...
Second, there's a set of graphics for an entity (enemy?) that was, I think, never actually used in the game. It's called Aleph. Aleph, of course, is the Hebrew letter A. The Aleph graphics include the Aquarian letter A inscribed on the forehead of a stone face somewhat similar to Creator's. The Aquarian A is also what appears over song-form Naija any time you sing the full Verse* (the song that the mother is singing in the sunken city, that you have to sing to open the last door there). If you hunt hard enough (clever usage of the grep command!) you can find that the only place Aleph is mentioned in the scripting for the game is as something that would be spawned by the final form of the creator -- except that the line of code that does that is commented out.
* The creator mentions at the end that his mother's song permeated everything he created, but he could never remember the chorus, only the verse. As Naija says at the beginning --
the Verse permeates everything and binds it together.
In any case, it looks like at some stage in designing the game, there was going to be some greater significance to the Aquarian A -- maybe something along the lines of the "I am the Alpha and Omega, the Beginning and the End" deity meme...
Also, it looks like there may've been an entire stage of the Creator battle that got cut... In the gfx/creator directory there's a subdir for "form3" that includes images that I'm pretty sure I never saw during the creator fight...
Any chance anyone might be able to get comments from Alec Holowka on any of this? The game is completely fantastic, I'd love to hear more about the development process, the backstory, etc. And I really hope a sequel is in development. I expect great things from Lucien!
Edited to Add: Another mystery -- who are Zunna and Vedha, as in Zunna's Perogi and Vedha's Cure-All and Sea-Crisp? In the graphics, Vedha shows up affiliated with a few parts of Naija's house, including the stand that the giant save crystal is on, and the kitchen hearth. Searching for Vedha in the resources found some interesting dialogue in a few entity scripts -- childDrask, childSharan, and childTeira. Are these entities that didn't get used in the game, or did I completely miss some interesting scene that would've given more backstory? There don't seem to be associated graphics for these entities... Similarly, there's a script for a Zunna entity (which looks like maybe it was a miniboss?), but no graphics.
Further addition: Aha! The dialogue file containing the Creator's last monologue -- where he's speaking in the voice of the little boy he once was -- is called "eric.txt". So I guess his name was Eric, before he was the Creator...