I agree - this was my one minor nit-pick after reading the post as well.

I'd love to see muddy maps for other past presidential elections if you can get a hold of the data (and this one too, once all the votes have been counted).

Really cool work, and well-explained!

I experimented a bit with the source code at https://github.com/tuttlepower/VotingMap , you can add an area correction by changing the line

    fillOpacity: (us_votes[i].total_votes / 59828),

to something like

    fillOpacity: (us_votes[i].total_votes / (59828 * 50 * (feature.properties.AREALAND / 5.195e10))),

But I think in practice, this effect is swamped by the "upper fence" effect described in the original post. In other words, the scale is very far from linear anyway, by changing the magic number 59828 above you can make it look dramatically different. I should really calculate what the (Q3 + 1.5 * IQR) value is, but above I just put in a "* 50" to make the overall impression of the map similar.

The resulting image: https://imgur.com/3K8Wwan