Separation of the footer from the columns is no problem here (cf Alt Layout 1). Reason: There is no body background image, thus no match-up issue when we mask the bottom of the columns.
The computations required to produce these (deliberately non-uniform) vertical borders and spaces would be prohibitive if one had to modify even a well-commented css text-file. Our main.css.php file performs all the calculations (e.g., a six-term negative margin) from base values entered in the css_vars file.
The columns, as always, are actually full height, made to seem less-than by masking, not margining. Their individualized top and bottom "borders" (cf top in Alt Layout 1) are made with absolutely positioned divs.