Thanks. I have noticed as well all this mess is because of Calibre when it converts ePub to ePub (to include the cover for instance or do some other stuff) changes the ePub structure a lot, with new css properties, and even edits the individual pages and add fixed margins to them.
Instead I have taken back the original file, I have added the cover manually with Sigil, and I have changed nothing more. And oh miracle, now the lines are good, I can change the line height from within my kobo, and the margins as well.
Now I'll avoid converting books with Calibre
