While writing this question and retrying to make sure I tried anything before asking here, I found the following solution.
It seems like Dartium (Chrome with a native Dart VM) has a bug (issue 12224) where changes to the viewBox are not reflected directly.
Adding the following code after changes to the viewBox forces Dartium to somehow resize to the requested size:
// add an empty ```<g>``` element to force svg resize
SvgElement g = new SvgElement.tag('g');
svg.append(g);