Since under the hood, a characters alignment is just G/N/E, and you folks (the Immortals) can gradually move the slider in one direction or another, are there many points of game mechanics that are affected by alignment beyond just “is good” or “is evil? Are there places where a character like Malthalia, for example (whose align was, according to Nep, lowered from good towards neutral) would experience more severe or less severe effects from something than a completely good person?

Mostly, alignment is alignment. In some sense, intermediate steps can be our way of saying "I saw something that really seems unbefitting this alignment, but it isn't enough by itself for me to do a full change." Enough of those incidents takes its toll.

A few things it does matter for. For example, an archon will get mad extremely quickly if you murder a 'real' good PC; it would (depending on who you were) react differently if you were to fight late-life Malthalia.