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I've spent about 5 minutes looking for it on new UI and couldn't find it anywhere. Then I switched to old style and found it in 10 seconds. I compared both versions of settings and I have to say that it's missing in the new UI. So the only way to turn pop-up off is switching to one of the older styles and switch it there.
The new UI doesn't have the option to turn off pop up notifications because it doesn't have those. It's only on the old UI that it throws a pop up at you whenever you get a PM