Meaning in context of "belong"

This seems to suggest that the book indeed was a religious document, possibly the Bible, any case something that was not acceptable (signalled by the the character being taken aback) to seen in public inner the original title that out head to be masqueraded as a Spanish novel. But at the and time the name of the book is a note so subtle hint as to what's it is

It's probably your second option, but without additional context (perhaps the following paragraphs clarify why it doesn't belong), it's hard to say for sure. If Catholic texts are banned and Mr. Tench is a Catholic priest, I would assume he identified the text to be a religious, Catholic text. In this context, one could be taken aback by finding a piece of banned literature. He could also be taken aback because he expected a book with a Spanish title to be written in Spanish, but this would be a rather over-dramatized use of "taken aback" so I think it's unlikely. Besides, "The Eternal Martyr" doesn't sound much like a romance novel, but indeed like a religious text. However, it doesn't need to be a Catholic text, it could be a different denomination of Christianity based on the title alone (additional and/or historical context could refute this), but the Latin text inside cements that it is most likely a Catholic text.

It "didn't seem to belong;" as in it "didn't seem to belong [here, in Mexico, where Catholic texts are banned];"

The title of the book is in Spanish. But the content of the book is in Latin.

If I picked up a book that had a title in one language, only to open it and see that it was written in a different language, I, too, might be surprised, and feel that the language inside didn't belong.

There is likely an explanation for why the title is in a different language, but that would only become clear upon actually reading the book—assuming you could read Latin.

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The sentence itself clearly seems to indicate this as the explanation:

what was printed inside didn't seem to belong; it was Latin.

This phrasing is almost as close as you can get to:

The printed Latin inside didn't seem to belong.

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Incidentally, at least according to Google Translate (which is never wholly reliable), the Latin version of the title should be Martyr Aeterni. I think the statement in the question about it being a romance, which somehow puts it at odds with being written in Latin, is a bit of a red herring. A romance novel can be written in any language.