Accepted answer

You could always sidestep the native d3 stack layout helper functions and compute the rect positions yourself from the data - here is a basic example of a stacked bar with data similar to yours:

You still need to do a little transforming of data, so it might still be worthwhile to try transforming to the layer inputs that d3.stack takes, but I present this in case it might be helpful.

stacked bar example without stack layout

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