Such tricks are aimed at the same sort of people who are the target for the badly-spelled-and-grammaticized text in 419 scam emails. Such people don’t tend to have a very good sense of the “formal etiquette of computer software vendors”, so to speak—they don’t know to expect that a system will be guaranteed to follow certain unchanging stylistic conventions.
To such users, an OS desktop is an unpredictable thing. Their (live) wallpaper and (dynamic) lock-screen background change out from under them at random. Their theme changes between Light and Dark (and they haven’t yet noticed the concordance with the time of day.) The Google Doodle changes without a seeming pattern (and they’ve never clicked on it to find out why.) Every once in a while, an app updates and looks entirely different after a restart. New application shortcuts appear seemingly at random on their desktop. Whenever their nephew “fixes” their computer, most of those disappear, and many other features get changed as well. Was it something the nephew did? Or were those just temporary, and disappear if you restart the computer? Or were they viruses?
Why would such a user even be surprised if, one day, the computer decided to change everything about their desktop out from under them while they were in the middle of watching a video? Par for the course. Computers are unpredictable.
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But also, it’s pretty easy to make the “desktop” part of the desktop irrelevant. The goal here is to re-invoke the concept that the user is looking at their OS chrome (i.e. “windowed mode”, rather than “fullscreen mode”); not that they’re looking at their desktop specifically.
So, in the video, just display a maximized Chrome window showing YouTube navigated to the innocuous “bait” video that was previously playing up to that point, as if the video had been first navigated to and then de-fullscreened. And then, show the pop-up window on top of that maximized Chrome window.
The only thing the video’s author needs to get right, at that point, are 1. Chrome’s window decorations, and 2. the taskbar.
(It doesn’t matter if the user isn’t using Chrome; even I, as a power-user, wouldn’t find it strange to find that something I had done had managed to install Chrome and force it to open a URL. Happens on Windows with things accidentally opening in Edge all the time. And lots of programs have dark-pattern installers that try to install Chrome for you; especially those of other Google products, e.g. Google Earth, Google Drive, etc.)