So I found out that the problem was related to an incompatibility between d3 and the current revision of the GeoJSON standard.
I know it has just been me talking to myself here, but for future readers who also run into this issue, the solution, and this is assuming you are using mapshaper, is to add the gj2008 flag to the -o command so that mapshaper will output clockwise rings. Reference: https://github.com/mbloch/mapshaper/issues/432#issuecomment-675775465