Miles,
See
http://bl.ocks.org/2997144 which is a derivative of your gist (thanks for that!). Definitely a WIP as the blurb is there before the implementation is done, but it's way past bedtime and what /is/ working is the 'sum' display I can see happening in pos+neg stacked bar charts: that is the sum of all the actual values (a.k.a. consolidated bottom line P/L), here plotted as a line, green for gain (profit), red for loss.
I hope the README.md that goes with it is clear on the train of thought: basic point is that there's no use case for the need to compare total bar heights (as in total height of pos+neg bar with the next couple); at least I can't, with a bit of brainstorming here, come up with any scenario that'll pass even the flimsiest reality check.
There /are/ scenarios that get close, but that's just bits of pencil on a napkin and the last part of the README blurb there; I still need to build that one as a working d3 chart. I know how it'll look -- brain already renders an image -- but now I need the time&effort to code it. I'm slow. Grmbl.
OT: Implicit (secondary) point of the blurb in that gist: think through what your chart users will be asking and want quick answers for; you might want to try and explore chart types that are not one-click out of the Excel box, when those might answer the envisioned/expected questions better/faster.
OT #2: I just /had/ to scratch my semicolon itch. I could yabber about Crockford and all that, but that would just be corroborating my feelings there.