Yeah I get what you're saying and the car makes a fair bit of other noises that I have learned to ignore, but this one just bugs me. I am currently using the stock upper strut mounts and do not see any signs of wear or movement on them when I shake the car. I attached some images of the upper mount. I know there is a concave washer and maybe that got installed the wrong way? It seems like it would always be noisy if that was the case though.
Here is a video where you can hear the clunk. Its the hollow sound. It can be heard best at 11,12,14,17 seconds. Sounds like someone is tapping the bottom of an empty 5 gallon bucket. thunk, thunk! I am pulling out of my garage in this video. It always happens when the front tires transition from the garage to the driveway where there is a small stress relief groove.
You can see where the coils are rubbing together. This is with the tire off and the spring uncompressed. Under the weight of the car those coils remain touching.