John-
When I first started working on dedupe, I was on the same line of thought as you - I should only see cluster_scores ABOVE the threshold. However, I think these are related to how the connected components eventually group (similar to how you stated), and the threshold helps inform them in the background. As far as if a low score should be "worrisome"... I am not sure. I definitely see some odd groupings at times but have my doubts that it is only the *lowest* scores that have the bad/odd groupings.
My understanding of this is pretty rudimentary, and I would appreciate being corrected if I am way off base here. So, I don't think I was a lot of help here, but I can commiserate with you if that is of any consolation. :)
-Matt Z