'em's and percentages are a must in my opinion if scripts are going to be used on flow layed out sites. A possible example of use could be dragging and dropping, where you calculate an elements position based on the pixel mouse co-ordinates, but then drop the element with percentage coordinates calculated from them.
But then updateNodeAttributes(elem, {'style': {'left': mouse.x/[screenWidth]+ '%', 'top': mouse.y/[screenHeight] + '%'}} would suffice. I wouldn't like to see MochiKit get too much stuff like this (that assumes a certain way of doing things, e.g. pixels), it seems to me to be extending the scope of the core library too much.