They can be made to be tightly coupled, but they're not necessarily intended to be. A lot of themes override core WordPress functions via a functions.php in the theme root directory. You don't have to include any core WP code in your theme, but WP provides an easy way to do it if you need to.

That WP would pursue this if not puzzles me.

IMHO, Mullenweg comes off looking like a brat in this whole mess. Regardless of the legality of the whole thing, this seems to be a straddling-the-line kind of situation, which makes it feel like there's some kind of ulterior motive at play.

Edit: This link from elsewhere in the thread totally changed my opinion. http://drewblas.com/2010/07/15/an-analysis-of-gpled-code-in-... Seems like Thesis should pretty clearly be GPL.