Clear does often have a precheck/non-precheck distinction, but when I had precheck (and not clear), I had enough trouble with miscommunications between different TSA agents about a line being one or the other that resulted in delays and secondary bag screening, at least at LAX, that it did not seem particularly useful. I did not appreciate being told by one person not to remove anything from my bag, then shouted at by another person for not having removed anything from my bag.
Most US airports I’ve been to have 4 types of queues:
* No TSA precheck, no Clear
* TSA precheck, no Clear
* No TSA precheck, Clear
* TSA precheck, Clear
They all work exactly as you expect (you get the benefits of either precheck or clear or both at once, depending on the queue).