I don't believe stacked bar is currently supported in the waterfall chart
There may be a way to hack the combo chart to look like a waterfall by using custom coloring to hide the bottom of the stack and make the bars appear to float. Sort of how Qlikview does the bar start. But I'd be reluctant to make something that complicated.
I believe VizLib is coming up with a waterfall chart soon. Probably other options in Qlik Branch as well
In case your question is still relevant, we have a Waterfall Chart in the AnyChart extension for Qlik Sense. In general, this tool is similar to the default QS Waterfall Chart but supports subcategories (shown as stacked sub-bars) and provides a wider range of options. Check out the AnyChart Waterfall Chart Documentation to make sure that's what you want.