I have the JLT catch can installed but surprised when it wasn't full yet the dealer confirmed that it lost 1.5 quarts in 3k miles (getting the valve covers replaced under warranty). Question, where is the oil going if its not being caught in the catch can? Is it a poor design by JLT?
No. Those are unrelated issues.
A catch can / oil separator is just catching oil that is vapor in the air of your crankcase. Every engine has oil vapor in the crankcase air, and its loss amounts to no more than a few ounces in an oil change interval - at most.
In older engines, it was just allowed to solidify and drip out the side of your crankcase. In your engine, that valve that allowed it to drip out is routed back to your intake, via a hose (which now has a baffled can installed in that circuit to catch it).
If you engine is burning/losing oil by the quart, its not escaping through the PCV valve. It’s leaking from the oil pan, crankshaft bearing, piston ring, cam bearing, valve bearing, or valve cover- the areas where you could lose/burn oil in large volumes.
The amount of oil caught by a separator is actually pretty small. The reason you see posters showing several ounces collected in a single oil-change interval is that the other source of moisture found in crankcase air is water- and in much higher concentrations than the oil. That’s why the separator collects what looks like chocolate milk- the same mess you get if you leave your oil drain pan out in the rain.