I notice that this analyzer is referred to quite often whenever people are discussing or trying to promote their own special layout. It's almost the default go-to analyzer.
It's nicely presented and all, but how are the scores actually calculated? The about page doesn't really explain.
If you put Mod-DH in to, it scores pretty much identically to Colemak, results are here. Even more bizarrely, Programmer Dvorak is deemed best of all (at least on the Alice corpus)!
I'm guessing it has a very simple algorithm based on distance from home positions, ignoring the fact that some keys are easier than others. I don't know how it treats other factors like bigrams, finger balance, rolls, etc, although it does create some reports on these.
I know scoring systems are subjective, but still.... although this tool is useful for generating charts and graphics, I think its overall score calculation is pretty useless.