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It's not that they don't understand it, it's that they don't want the average user to have a convenient way to control this setting. Prompting the user for permission would give the user a very convenient way to keep it disabled for most websites. It's as simple as that.

Think about it this way: Which is more tedious: going into the settings and enabling and disabling webGPU every time you need it or a popup? Which way would see you keeping it enabled?

Its tyranny of the default with an extra twist :)