Some other differences I have noticed (specifically applies to PRS 505):
epubs have a very small auto-calculated page number in the right margin. I find this annonying.
Commericially produced epubs tend to have a blank line between paragraphs, whereas LRFs do not (they use indented paragraphs instead); I have no idea why this is so. This may be why Calibre has the option to remove blank lines between paras, but only for epubs (I believe Calibre replaces the blanks lines with an indent para).
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