I would not use an embedded font for a single character that should match the rest of the text. If it were the case of a Japanese character, then it's OK, because the Latin script and the Japanese characters are different anyway. But in this case it is a Latin character that will be used together with other characters in a potentially different font (even if you try to match the default font in your reader, it will not be the same font in other devices, particular in those that allow the user to choose a different font).
So, in this case I would probably use a single embedded font (one that includes the "ō" character) for the whole book. It would be easy to remove if someone is using a device that can display the "ō" without embedded fonts, and it wouldn't add unnecessary markup.
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