Thanks for your reply! I used Adobe Acrobat as a pdf reader. What is strange in your answer about pdf not having line height is that both of the pdf shown above have been created via calibre from the same epub (but with different conversion settings, I lost the settings I used for the pdf with the none overlapping highlights).
Because I didn't change Adobe Acrobat settings, that the source is the same and the only that changed between the two pdfs are the conversion settings in calibre, I was looking at the calibre settings as the culprit.
But what you seems to say is that, the conversion process as no control over the highlight heights, is that correct?
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