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...I had a single speed Bianchi, with a flip flop rear hub for either fixed or freewheel. It had a similar "klunk" that used to happen intermittently, when using it in the freewheel position. I was able to narrow the source down to the freewheel (which was not a great quality freewheel to begin with), by flipping it over to the fixed gear position, when the noise disappeared. In your case, with the setup you have, I don't know how you would do it, without swapping out a better quality freewheel to see. FWIW, even though freewheels are rarely the source of such noises, the quality of some of the newer ones is so poor that they do become a possibility.
I can't imagine they used a high quality freewheel on your bike at that price point.
With the whole disc brake setup you have going on, I'm not sure you can just swap in another wheel as a test. Good luck with it.