I just use 100%
Gulf canning wax (paraffin) and Shimano XTR chains. I change them out every 200 to 300 miles, and I don't have this noise problem. I wonder if for some reason the Shimano XTR chain is more amenable to waxing? It has some sort of special bonded teflon coating, and I have often wondered whether the wax (or whatever lube) simply seals the exterior of the chain, and protects this interface. I ride a lot of off-road conditions, but avoid getting the chain wet (rain is seasonal here in Coastal CA; it won't rain again until Oct or Nov). Those are the only differences I can think of. The life of my chains has at least tripled since I started doing this, FWIW.
I get up around 0.75% to 1.0% stretch sooner than I would expect.
How many gears? Mine is 11-speed. I never let the chain go further than 0.50%. If you do, the problem may be you have trashed out the cassette and/or sprockets.