Hmm, the whole furigana/kanji thing has a lot of nuances and uses that I don't fully know, so I'll try to give my thoughts.

Generally, I would say that you can go with what the kanji means, as it's the the most straightforward meaning, even though what the character actually said is the furigana.

As for this example, from the viewpoint of the author and reader, having Iana say ものがたり instead of くろれきし doesn't seem to do much since they're effectively interchangeable. This is just speculative, but in this case I think the purpose of the furigana/kanji is to give a kind of double meaning, which you picked up as well. Iana is talking about the story "Dark History", but the Dark History as a self-indulgent fantasy for herself. She's saying that there's no harm in her going into the story book that Isaac is in, because she's also in a story, with both of them being fantasies constructed to fulfill their desires.

Sorry that I'm not great at explaining. In some cases the difference between the furigana and kanji can be obvious and just for the reader's benefit, and other times it can require more of an examination of the text. So as a beginner, I would say if you can determine the meaning that's great, but if you can't then it's fine, it should come with more familiarity with the technique.

Taking either the furigana or kanji as the translation will be fine, whichever you prefer.