Note that there are several hands in that book. A date (1492) is written on the first page (scan 3), in the margin of what is already a messy flyleaf. This is not in the main hand. There are more hands involved in the later part of the book, which is where I first came across the interesting bits (last page and the one with the square charm drawing).
The parts that contain .O. go from ca. scan 439 to scan 449. They are part of a (sub)section starting You are not allowed to view links.
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Login to view. The page starts with some obligatory religious stuff, after which the true contents begin. I am not good enough at deciphering this kind of Latin, but JoeyB helped me out a bit through LLM text recognition, and we think the section is a treasure seeker's guide. (Take this with a grain of salt until confirmed!)
Each paragraph is something like "go to this or that mountain, look for the statue of a lion, take five steps east and you will find [treasure]". For example, on scan 438 linked above, the one but last paragraph describes looking for certain statues and you will have "inestimable sun and moon". We suspect "sun" is used in its sense of "gold" here, and that later paragraphs substitute this with the circle .O.. Normally the symbol for Sun is a circle with a dot inside, but this is the best I've got so far. So current hypothesis: it stands for gold.