It isn't smart enough to factor in the France thing, it just shows France that way basically because the teams in their group are either way above France or way below France (usual caveats about volatility in RP, incl for Argentina atm) - like Italy's situation, but not so extreme. Also it's just a fluke that there is *not quite* a 25% chance of France beating England, Wales or Australia, and *not quite* a 25% chance of finishing below Argentina. (as you can see better in the other versions).
As for the difference between the 2nd and 3rd versions... In small font, because I'm talking about minor details in the fine print
First of all note that the end of the whiskers show where there is at least a 2.5% chance (2.5% above and below, so 95% in between. A common choice for confidence intervals / error bars)
I'll use Italy as an example how the 2nd version works... they have a 0.17% chance of being at least 2nd in pool - way below 2.5%, so basically the same as no chance. Then they have another 95% or so chance of being exactly 3rd in pool.
So where does 2.5% fit in between them? well in total within the "3rd in Pool" area, there's 2.33% above 2.5%, and about 93% below the whisker tip at 2.5%. 93% is way bigger than 2.33%, and in the interpolation, the "3rd in Pool" area on the graph is split in that ratio, so the whisker goes to only a tiny distance away from the border with "2nd in Pool".
I didn't like this, because having the whisker extend nearly into the "2nd in Pool" area seems like it suggests there's a nearly 2.5% chance of making 2nd in pool - which there isn't.
The 3rd version weights the 2.5% 9x more than the next 22.5%, so e.g. New Zealand or Wales have a 0% chance of doing better than Champions, and a ~25% chance of being Champions. This basically means the tip of the whisker is decided equally by the 0% as by the 25%. To reach close to the top or bottom of an area, there needs to actually be a large fraction of a 2.5% chance of a result in the next area. E.g. Canada has a 2.46% chance of making 3rd in pool, so they still get to have a whisker almost reaching the line.
Not so mathematically elegant, and maybe a bit contrived, but what you think you're seeing when you look at it is more like what I'm actually trying to show. (Or at least that's what *I* see when *I* look at it. Do you see it the same?)