Thanks for the feedback - I agree that I need to do some work on how the axes scale and where the ticks go, and I see the bug you are talking about with the axis being greater than the sum. I think it is due to the placement of the tick. The very top of the axis is 99.8 but the label gets placed a bit lower so it looks like that. Will sort that out.
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You don't have to override the template in the lua code to include the mvp.css file. use --css argument to set the location of the css file. it can even take multiple arguments (one for mvp.css and one for chartss.css).
In the current state, your "function Doc(" block upsets existing pandoc workflows.
Edit: didn't want to sound harsh with only the criticism :) Thank you for showing how to use lua-filters to do really cool stuff. I've playing with lua-filters, but your code is a clear example of how to extend markdown with a mini-DSL.
Edit 2: Sent you a PR on github with what I was suggesting here.