McCloud is playing with the compositional rhythms allowed by the web. Normally a comics artist is constrained by whatever page size she's using for the book; McCloud is completely and utterly fascinated* by the possibility of breaking that long-standing constraint.
The repetition of regular squares sets up rhythms, that he then violates for purposes of mood, emphasis, timing, etc.
*seriously, his second comic about comics, "Reinventing Comics", basically boils down to "the Internet will transform the finances behind comics via micropayments" (right on the transformation, wrong on the micropayments) and "the Internet will transform the layout of comics by freeing us from the constraints of a particular page size".
The repetition of regular squares sets up rhythms, that he then violates for purposes of mood, emphasis, timing, etc.
*seriously, his second comic about comics, "Reinventing Comics", basically boils down to "the Internet will transform the finances behind comics via micropayments" (right on the transformation, wrong on the micropayments) and "the Internet will transform the layout of comics by freeing us from the constraints of a particular page size".