In reference to Judeo-Christian ethic and belief, I don't think there is really much ambiguity at all in the lyrics. Maynard does not believe.

His struggle is with his mother's belief, not his own. For most of the references to her, I think he was basically incredulous as to why she would believe in the face of what she was handed in life. For WFM/10,000 Days he was simply granting her a measure of respect within her own belief, not accepting it or converting to it in any way. It's called a temporary belief system, and he used a similar device before in 46+2 to entertain an extended metaphor for human & personal evolution.

Organized religion disgusts him because it left one of its most devout followers (Judith) out in the cold for more than a quarter of a century. This informs lyrics which directly challenge or reference theology, such as Jerk-Off, Opiate, Eulogy and Flood.

As to whether the lyrics are mere nonsense to make money, I question such a conclusion when dealing with a band that basically flouted every standard in the industry (except for being "melodic") and yet were a complete financial success anyway. When they signed their original contract with Zoo they insisted on complete artistic control over media, promotion, artwork, videos, Etc. This is usually the first thing to be handed over to the majors by bands that are desperate to sell out so they can get on MTV. Tool took less money for this, and have benefitted greatly because of it. In my opinion, the psychological ambiguity in their lyrics isn't really the money-maker. it's the sound and the melody that people enjoy (DESPITE the lyrics) which has made them millions.