I don't know if that word is used often. However, when you say "yes", you are verifying that there is some sense of truth and validity in the "understanding" of whatever is being discussed. In other words, "Is this understanding truly what they mean?" So, your "yes" or "no" determination does not have to be based upon faith or fact. Do you think their understand is possibly or probably what they mean. Hope this helps.

This construction is very odd. I think it means the same as: Is this understanding of what they mean [to say] believable? But using "understanding", "believe" and "mean" make this almost not intelligible English, IMO.