And that the person might be the source of preference. This is fairly important.

This is actually wrong. Whatever the AI starts with is its formal preference, it never changes, it never depends on anything. That this formal preference was actually intended to copycat an existing pattern in environment is a statement about what sorts of formal preference it is, but it is enacted the same way, in accordance with what should be done in that particular case based on what formal preference tells. Thus, what you've highlighted in the quote is a special case, not an additional feature. Also, I doubt it can work this way.

But, in any case, FAI theory is only here as an intuition pump for evaluating "what would the best thing be, according to this person's implicit preferences?"

True, but implicit preference is not something that person realizes to be preferable, and not something expressed in terms of confused "ontology" believed by that person. The implicit preference is a formal object that isn't built from fuzzy patterns interpreted in the person's thoughts. When you speak of "contradictions" in person't beliefs, you are speaking on a wrong level of abstraction, like if you were discussing parameters in a clustering algorithm as being relevant to reliable performance of hardware on which that algorithm runs.

If it is possible to have preference-like things within a fundamentally contradictory belief system, and that's all the human in question has, then knowing about the inconsistency might be bad.

A belief system can't be "fundamentally contradictory" because it's not "fundamental" to begin with. What do you mean by "bad"? Bad according to what? It doesn't follow from confused thoughts that preference is somehow brittle.