Yeah, I think it's clear they're entirely separate. One is clearance level, the other is threat level. It seems pretty clear that, if something is a threat level 7, more than just level 7 clearance would be involved - it'll be an all hands on deck type situation. To make it clearer, Threat Level 7 seems to be analogous to DEFCON 1, while Level 8 Clearance seems to be analogous to "Top Secret" clearance (although both seem to rely on Compartmentalizing information, so they'll have Special Access Programs on top of the levels of secrecy).
The clearance level thing, iirc, was created in the one shots and adopted into the series as a major component. Threat level was only said in the Avengers, if I'm not mistaken. I don't think the Overkill device required SHIELD to be at Threat Level 8 based on any dialog and I agree that the Tesseract is more significant of a threat than the Overkill device. The Overkill device had a high level of clearance because it involved sensitive political issues and was a covert operation, not because it was the more serious threat (which, as I said, would seem to necessitate greater sharing of information, not less).
I'll agree that the terminology is confusing, but, unless I'm misremembering something from The Hub, the terms have at least been kept separate and are, by themselves, relatively logical.