"Document default" means to use the fonts that embedded in the book. Selecting one of the one of the other fonts, overrides this. The times I have seen this problem, the book embedded a Charis font. From discussions around here, there are versions of this that have been fiddled with to use different font metrics. I think some of these may result in the renderer getting the position of the text wrong.
As a simple example of what I mean, have a look at where the title of the book is displayed when you use different fonts. With "Georgia", the title is centred with the home and other buttons. With "Gothic" it is displayed noticeably lower. The exact positioning of the letters in a line is at least partly defined by something in a font. I think that if you extracted the embedded font and added it to the device, you would see something similar.
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