Ok. I solved it modifying more deeply all the css files inside the data folder. I still don't know if the epub.css is the only one responsible for changing the format in the epub files (I would assume so, but I am not sure since I was having problems with it). In the end I have used the style that I like in all the css files. Important modifications:
Code:
p { text-align: justify; text-indent: 1.2em; margin-top:0em; margin-bottom: 0.4em }
.justindent { text-align: justify; text-indent: 1.2em; margin-top:0em; margin-bottom: 0.4em }
I also added the margin-bottom value in all the styles in my cr3.ini