(This question arose because on some other SE many of us tried to translate this expression. It turns out it was not so easy, and it would certainly help if we had a better grasp on it.)
I believe this expression can be used with two different purposes, but I might be wrong. Am I right to assume it can be used:
a. To express a doubt about a given hypothesis:
Some say they are professionals, though you wouldn't think it from the way they acted.
b. Or sometimes to doubt about the legitimacy/value of an hypothesis:
It turns out they are professionals, though you wouldn't think it from the way they acted.
To warn about (or notice) a possible prejudice:
They truly are capable, though you wouldn't think it from the way they acted.
If I'm right, the difference is perceptible because in cases 1. a. and 1. b. the hypothesis is weakened whereas in case 2. the hypothesis is strengthened.
Also, in the light of a related question, it seems that no difference of meaning arise directly from a choice between pronouns it and that to refer to a main clause. However my feelings tell me that that could a better fit for the 1st purpose (especially case b.), and might help to disambiguate when the context fails to do so.
Any comments or further light on the matter would be appreciated!