Frankly I don't care what the user guide of Calibre claims. Like I said before, I don't like the code from Calibre. For conversion it is ok, but I always cleanup afterwards. All the additional margins in every styles is annoying. It will override almost al settings you made due to the cascading.
I see where the problem arise and you could try to issue a bug to Kovid.
For your problem at hand, you can try the following. In sigil open the stylesheet and do a replace of the lines below with nothing. It is not a perfect solution, that would be a total cleanup of code.
Remove the following lines in the stylesheet of all classes:
Code:
border-bottom: 0;
border-top: 0;
display: block;
margin-bottom: 0;
margin-left: 0;
margin-right: 0;
margin-top: 0;
padding-bottom: 0;
padding-top: 0;