Your linked site for some reason doesn't include fallout by default, nor does it seem to factor casualties from it. Turn on fallout + surface burst, and a 100MT bomb's deadly fallout range goes from the center of France (where the label is on their map) to the center of Germany and I suspect that's an extreme underestimation, especially the conic they give.
It's also possible that the NYTimes is conflating facts by accident. Your demo link only accounts for single big-blast effects but the way you optimize damage with nukes is lots of smaller bombs, often in a single bomb - MIRV is one name for this. The reason is pretty simple. We approximate the explosive range as a sphere and the volume of that sphere is proportional to the cube (^1/3) of the yield.
So if you increase the yield by 10x you only increase the explosive radius by something like 2.15x. On the other hand, detonate 10 bombs side by side and you increase the radius by 10x. This not only maximizes damage, but also works to further nullify any sort of anti-missile defense. And 100MT would be well more than enough to obliterate France.
You can also kind of intuit this by thinking about 100MT means. That's 100,000,000 TONS of TNT explosive capacity. That's about 1.5 tons of TNT for each and every person in France. That's just a stupidly massive absurd amount of destruction.