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You cannot have different settings for each book. The problem is that some books use a smaller size for the body text which is not a good idea. It's best to just use the default font size. But even the BPHs do this.
Your solution is to edit the CSS to change the main font size to the default (as in no specified font size). Then all your books will have the same body font size. You can do this with Calibre's eBook Editor as long as the eBook has no DRM.
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