I have exactly the same issues. As you say, calibre adds the blank lines when converting to lrf even if it works fine when converting to epub. I can't imagine why, maybe it's the <span> madness.
I am also a linux user. FYI, bookdesigner does work under wine (I use a commercial version, Codeweavers). Mind you install internet explorer 6.0 first. It's by far the best tool there is for getting lrf right. But, you have to learn how to use it and it's not very intuitive, although you can find an excellent tutorial on this forum.
You edit html by hand simply opening the file with a text editor. Kate, gedit or gvim, for example.