http://code.google.com/p/tullamods/wiki/DominosAdvanced

Dominos includes a feature that allows you to set a bar to become partially, or even fully transparent when the bar does not have focus.

This is currently not true. I can create a bar with this functionality. However, the entire bar will disappear when the mouse moves from a button which has something on it, to a button which is empty.

Interestingly, when the mouse has something 'grasped', like when I'm dragging an item, the bar does stay visible.

The going out of focus when over an empty button is intentional, since its a clickable space.

Aah, I see how this is true in cases where I overlap bars and I can click through one bar with no button into another one with a button.

So my recourse would be to make an empty macro and drop it in those places, or is there something different I could do?

You could also potentially do something with showing empty buttons + a custom empty button texture.