Most of his writing is freelance and ghostwriting, but I do believe he has a novel finished (although not yet published), but I'll let him respond in more depth when he can.
The way I interpret it is this. Keep in mind this is just my interpretation and the writer may have meant something totally different (although I should also mention we did collaborate on the outline so I did have some input in writing the story), but this is what I think of what I think of the meaning of the game:
The universe (of the game, and the current one if you like) is composed of things and their connections, symbolized in the game by Indra's Net (those green lines which connect objects when you move away from them). Indra's Net also has a mythology (see the link to it in the footer of the game's website) -- basically an infinite number of pearls, each of which reflects every other single pearl, and each reflection also reflects every other single pearl, such that in one single pearl the entire universe is contained. The real-life Gutei's finger story, at least to me, means reality is one; like Indra's net, it means that every single part of the universe implicitly contains the rest of it. So Gutei and Indra are saying the same thing, only they say it in different ways: Indra focuses on the infinite number of things and their, Gutei focuses on one thing, but the idea is the same.
Aa had a problem with and eventually (after he "died" / descended into Hellspace) rejected those connections, wishing to break down the net and make it a simple line instead. Most mental problems I believe begin with rejecting reality -- not usually even in the sense of not believing in it, but just in the sense of not liking it or selectively focusing on illusions and things which don't exist and disliking and being uncomfortable with things that do exist. Aa goes down this path first, then the player's character follows, although both go have different ways of degeneration (Aa focusing on being worshiped, the player's character focusing on protecting a non-existent granddaughter and planet). So both came to reject Indra's Net.
The main character, operating as Indra's Finger in Hellspace, and Aa, leading Gutei's Finger, confront each other in the final section of the game. Aa uses the Hate Point -- which rejects other Points and weakens them, and the player's character uses the Love Point, which embraces other Points and strengthens them by forming connections. The Hate Points become Love Points. Aa refuses to accept it. It's not clear whether the player's character accepts it or not, but I like to imagine he does, because at the end all the Love Points are connected to him.
We do plan a sequel, but it'll be awhile coming -- we're going to make a few other games in between.