Just a small point-- tolerating tolerance seems to me to be a less powerful tool than the principle of charity, of which plenty has been said on this site. For me, the image:

One of the likely characteristics of someone who sets out to be a "rationalist" is a lower-than-usual tolerance for flaws in reasoning.

doesn't even start to feel right for me from a 'should' perspective (though it is quite familiar from an 'is' perspective). My image of a rationalist is someone exceptionally concerned with making sense of what others are saying, because arguments are not battles.