Petr, I hope you are well again.
@"experimental theme that is using YUI grids" You surely remember what I wrote about YUI grids - YUI grids are too specific.
And
1.) The "Holy grail ..." offers the 2-1-3 column layout which delivers content first before the side columns. With the way Moodle pages are calculated and rendered in 2.0 it is even more important to send the content before the side columns are calculated and rendered. Does the YUI grid offer this option?
2.) The "Holy grail ..." offers equal hight columns. Based on it I can implement the "lines" and "color" theme in 2.0 which depend on equal hight columns. Does the YUI grid offer equal hight columns?
Another approach
Instead of forcing a layout as the one and only solution there might be a commitment to officially support different layouts - for example the YUI grid based layout and the "Holy grail ..." layout. Pairing the layout.php scripts with the fitting layout.css would make sense and increase flexibility. Fonts, colors, module specific CSS etc. can be placed in other CSS files. You may choose one or the other layout.php/layout.css pair and use the same other CSS files.
Designers could better choose the base layout fitting their design needs. And would not be forced to implement strange named grids.
If this "open" approach might be chosen it doesn't really matter that much, which layout you use for the base theme in Moodle.