You've stumbled on one of the basic problem with widgets, and it's one of the reasons that both Laza and I dislike them.
In short, the page produced by the skin developer doesn't know that the widgets are there, and the skin has very little control over their appearance. A skin could leave a default amount of space available for the widget comment box, but then if that box is minimized, the skin's own display is no longer taking full advantage of the viewport.
Trying to make a skin fully responsive to the size of the viewport is tough enough, but trying to compensate for what some other script is doing to the display is more than we're willing to tackle.
In my skins, I finally got tired of trying to work around the widgets, so my skins disable them completely.
And BTW, because HTML, by its very design, is a "start at the top and lay out the elements down the page" language, putting stuff on one side or the other is particularly challenging!