Use isobands in the "smooth" representation (so that the fillOpacity parameter makes sense)

[mthh]

Currently, the contour polygons generated by d3.contours include all points above a given threshold value (instead of isobands which include all points between two given values).
This causes the different features in your contour layer to overlap.

So, when I set fillOpacity to 0.3 (for example to see, by transparency, the administrative units below) it makes a weird rendering, since the entities overlap, and it makes it impossible to see the entities under the smooth representation (where the lowest class does take transparency into account, but due to the overlap between entities in the contour layer, it becomes impossible to see through entities in higher classes).
See for example your Cholera Map in https://observablehq.com/@neocartocnrs/smooth (where we can't see through the polygons, except for the lowest level in green, despite a fillOpacity of 0.3)

You could consider turf-isobands rather than d3 contours to generate the contours.

[Fil]

d3/d3-contour#71